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PDB | 2B43 | Crystal structure of the Norwalk virus RNA dependent RNA polymerase from strain Hu/NLV/Dresden174/1997/GE

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Internal ID
31907
PDB Entry ID
2B43
Title
Crystal structure of the Norwalk virus RNA dependent RNA polymerase from strain Hu/NLV/Dresden174/1997/GE
Authors
Hogbom, M.,Rohayem, J.,Unge, T.,Jones, T.A.
Primary Citation
AuthorsHogbom, M., Rohayem, J., Unge, T., Jones, T.A.
TitleCrystal structure of the Norwalk virus RNA dependent RNA polymerase from strain Hu/NLV/Dresden174/1997/GE
JournalTo be Published
AbstractView
 
History
Deposition: 2005-09-22Release: 2005-10-04Last Modified: 2011-07-13
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
2.300.1960.1920.257P 21 21 21
Unit Cell
Length [Å]a90.47b125.56c218.13
Angles [°]alpha90.00beta90.00gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1non-structural polyproteinA, B, C, D
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1NorovirusEscherichia coli
SCOP Classification
CATH Classification
Structural Details
KeywordViral protein
TextRNA, polymerase, Viral protein
 
Polymeric Molecules
Chain A
Descriptionnon-structural polyprotein
Polymer typepolypeptide
Formula Weight58658.4
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Chain B
Descriptionnon-structural polyprotein
Polymer typepolypeptide
Formula Weight58658.4
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Chain C
Descriptionnon-structural polyprotein
Polymer typepolypeptide
Formula Weight58658.4
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Chain D
Descriptionnon-structural polyprotein
Polymer typepolypeptide
Formula Weight58658.4
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aA,B,C,Dpolypeptide(L)n/a
Natural/Genetically Modified Source
Scientific NameNorovirus
Source GenusNorovirus
Host Common Namen/a
Host Scientific NameEscherichia coli
Host GenusEscherichia coli
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Crystallization Experiments
MethodVAPOR DIFFUSION, SITTING DROP
PH6.5
Temperature298.0
DetailsSodium Citrate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
90.47125.56218.13
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.0090.00
Space Group
P 21 21 21
Diffraction Detector
DetectorCCD
TypeMARRESEARCH
Detailsn/a
Collection Date2005-07-17
 
Diffraction Radiation
MonochromatorSilicon (1 1 1) channel-cut
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List0.94995
 
Diffraction Source
SourceSYNCHROTRON
TypeESRF BEAMLINE ID23-1
SiteESRF
BeamlineID23-1
 
Reflection Details
Observed Criterion Sigma (F)0.0
Observed Criterion Sigma (I)0.0
Resolution (High)2.30
Resolution (Low)30.00
Number Reflections (All) 107725
Number Reflections (Observed)107725
Percent Possible (Observed)97.1
R Merge I (Observed)n/a
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancy5.0
 
High Resolution Shell Details
Resolution(High)2.30
Resolution(Low)2.40
Percent Possible(All) 95.70
R Merge I(Observed)n/a
Mean I Over Sigma(Observed)3.1
R Sym I(Observed)0.374
Redundancy3.3
Num Unique Reflections(All)12568
 
Refinement Statistics
Structure Solution MethodMOLECULAR REPLACEMENT
Resolution (High)2.30
Resolution (Low)20.00
Cut-off Sigma (F)0.0
Cut-off Sigma (I)n/a
Number of Reflections (All)102225
Number of Reflections (Observed)102225
Number of Reflections (R-Free) 5372
Percent Reflections (Observed)97.18
R-Factor (All)0.19554
R-Factor (Observed)0.19554
R-Work0.19232
R-Free0.25654
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value31.932
Anisotropic B[1][1]1.19
Anisotropic B[1][2]0.00
Anisotropic B[1][3]0.00
Anisotropic B[2][2]0.44
Anisotropic B[2][3]0.00
Anisotropic B[3][3]-1.63
 
Resolution Shells
Shell Resol (High)2.30
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)387
Number of Reflections (R-Work)7251
R-Factor (R-Work)0.230
R-Factor (R-Free)0.294
R-Free Errorn/a
Percent Reflections (Observed)95.25
 
RMS Deviations
Parameter TypeDeviation From Ideal
r_bond_refined_d.012
r_angle_refined_deg1.433
r_dihedral_angle_1_deg6.531
r_dihedral_angle_2_deg37.713
r_dihedral_angle_3_deg18.227
r_dihedral_angle_4_deg20.262
r_chiral_restr.102
r_gen_planes_refined.005
r_nbd_refined.218
r_nbtor_refined.305
r_xyhbond_nbd_refined.173
r_symmetry_vdw_refined.176
r_symmetry_hbond_refined.158
r_mcbond_it.676
r_mcangle_it1.106
r_scbond_it1.616
r_scangle_it2.624
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms15716
Nucleic Acid Atoms0
Heterogen Atoms0
Solvent Atoms1122
 
Programs
Data Collectionn/a
Data Reduction (intensity integration)XDS
Data Reduction (data scaling)XSCALE
Structure SolutionMOLREP
Structure RefinementREFMAC 5.2.0005
 
Software
Classificationrefinement
Software NameREFMAC
Software Version 5.2.0005
 
Sequence Chain
A
Sequence
  1   MGGDSKGTYC  GAPILGPGSA  PKLSTKTKFW  RSSTTPLPPG  TYEPAYLGGK  DPRVKGGPSL

 61   QQVMRDQLKP  FTEPRGKPPK  PSVLEAAKKT  IINVLEQTID  PPEKWSFTQA  CASLDKTTSS

121   GHPHHMRKND  CWNGESFTGK  LADQASKANL  MFEGGKNMTP  VYTGALKDEL  VKTDKIYGKI

181   KKRLLWGSDL  ATMIRCARAF  GGLMDELKAH  CVTLPIRVGM  NMNEDGPIIF  ERHSRYKYHY

241   DADYSRWDST  QQRAVLAAAL  EIMVKFSSEP  HLAQVVAEDL  LSPSVVDVGD  FKISINEGLP

301   SGVPCTSQWN  SIAHWLLTLC  ALSEVTNLSP  DIIQANSLFS  FYGDDEIVST  DIKLDPEKLT

361   AKLKEYGLKP  TRPDKTEGPL  VISEDLNGLT  FLRRTVTRDP  AGWFGKLEQS  SILRQMYWTR

421   GPNHEDPSET  MIPHSQRPIQ  LMSLLGEAAL  HGPAFYSKIS  KLVIAELKEG  GMDFYVPRQE

481   PMFRWMRFSD  LSTWEGDRNL  APSFVNEDGV  EVDKLAAALE  HHHHHH  

Sequence Chain
B
Sequence
  1   MGGDSKGTYC  GAPILGPGSA  PKLSTKTKFW  RSSTTPLPPG  TYEPAYLGGK  DPRVKGGPSL

 61   QQVMRDQLKP  FTEPRGKPPK  PSVLEAAKKT  IINVLEQTID  PPEKWSFTQA  CASLDKTTSS

121   GHPHHMRKND  CWNGESFTGK  LADQASKANL  MFEGGKNMTP  VYTGALKDEL  VKTDKIYGKI

181   KKRLLWGSDL  ATMIRCARAF  GGLMDELKAH  CVTLPIRVGM  NMNEDGPIIF  ERHSRYKYHY

241   DADYSRWDST  QQRAVLAAAL  EIMVKFSSEP  HLAQVVAEDL  LSPSVVDVGD  FKISINEGLP

301   SGVPCTSQWN  SIAHWLLTLC  ALSEVTNLSP  DIIQANSLFS  FYGDDEIVST  DIKLDPEKLT

361   AKLKEYGLKP  TRPDKTEGPL  VISEDLNGLT  FLRRTVTRDP  AGWFGKLEQS  SILRQMYWTR

421   GPNHEDPSET  MIPHSQRPIQ  LMSLLGEAAL  HGPAFYSKIS  KLVIAELKEG  GMDFYVPRQE

481   PMFRWMRFSD  LSTWEGDRNL  APSFVNEDGV  EVDKLAAALE  HHHHHH  

Sequence Chain
C
Sequence
  1   MGGDSKGTYC  GAPILGPGSA  PKLSTKTKFW  RSSTTPLPPG  TYEPAYLGGK  DPRVKGGPSL

 61   QQVMRDQLKP  FTEPRGKPPK  PSVLEAAKKT  IINVLEQTID  PPEKWSFTQA  CASLDKTTSS

121   GHPHHMRKND  CWNGESFTGK  LADQASKANL  MFEGGKNMTP  VYTGALKDEL  VKTDKIYGKI

181   KKRLLWGSDL  ATMIRCARAF  GGLMDELKAH  CVTLPIRVGM  NMNEDGPIIF  ERHSRYKYHY

241   DADYSRWDST  QQRAVLAAAL  EIMVKFSSEP  HLAQVVAEDL  LSPSVVDVGD  FKISINEGLP

301   SGVPCTSQWN  SIAHWLLTLC  ALSEVTNLSP  DIIQANSLFS  FYGDDEIVST  DIKLDPEKLT

361   AKLKEYGLKP  TRPDKTEGPL  VISEDLNGLT  FLRRTVTRDP  AGWFGKLEQS  SILRQMYWTR

421   GPNHEDPSET  MIPHSQRPIQ  LMSLLGEAAL  HGPAFYSKIS  KLVIAELKEG  GMDFYVPRQE

481   PMFRWMRFSD  LSTWEGDRNL  APSFVNEDGV  EVDKLAAALE  HHHHHH  

Sequence Chain
D
Sequence
  1   MGGDSKGTYC  GAPILGPGSA  PKLSTKTKFW  RSSTTPLPPG  TYEPAYLGGK  DPRVKGGPSL

 61   QQVMRDQLKP  FTEPRGKPPK  PSVLEAAKKT  IINVLEQTID  PPEKWSFTQA  CASLDKTTSS

121   GHPHHMRKND  CWNGESFTGK  LADQASKANL  MFEGGKNMTP  VYTGALKDEL  VKTDKIYGKI

181   KKRLLWGSDL  ATMIRCARAF  GGLMDELKAH  CVTLPIRVGM  NMNEDGPIIF  ERHSRYKYHY

241   DADYSRWDST  QQRAVLAAAL  EIMVKFSSEP  HLAQVVAEDL  LSPSVVDVGD  FKISINEGLP

301   SGVPCTSQWN  SIAHWLLTLC  ALSEVTNLSP  DIIQANSLFS  FYGDDEIVST  DIKLDPEKLT

361   AKLKEYGLKP  TRPDKTEGPL  VISEDLNGLT  FLRRTVTRDP  AGWFGKLEQS  SILRQMYWTR

421   GPNHEDPSET  MIPHSQRPIQ  LMSLLGEAAL  HGPAFYSKIS  KLVIAELKEG  GMDFYVPRQE

481   PMFRWMRFSD  LSTWEGDRNL  APSFVNEDGV  EVDKLAAALE  HHHHHH