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PDB | 3NCV | NgoL

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Internal ID
72514
PDB Entry ID
3NCV
Title
NgoL
Authors
Namadurai, S.,Jain, D.,Nair, D.T.
Primary Citation
AuthorsNamadurai, S., Jain, D., Kulkarni, D.S., Tabib, C.R., Friedhoff, P., Rao, D.N., Nair, D.T.
TitleThe C-terminal domain of the MutL homolog from Neisseria gonorrhoeae forms an inverted homodimer
JournalPlos One, v.5, pp.e13726 - e13726, 2010
AbstractView
Pubmed21060849
DOI10.1371/journal.pone.0013726
 
History
Deposition: 2010-06-05Release: 2010-12-08Last Modified:
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
2.400.2210.2160.272P 1 21 1
Unit Cell
Length [Å]a49.50b62.10c92.10
Angles [°]alpha90.00beta104.60gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1DNA mismatch repair protein mutLresidues in UNP 460-658A, B
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Neisseria gonorrhoeaeEscherichia coli
SCOP Classification
CATH Classification
Structural Details
KeywordHydrolase
Textendonuclease, repair, dimer, Hydrolase
 
Polymeric Molecules
Chain A
DescriptionDNA mismatch repair protein mutL
Fragmentresidues in UNP 460-658
Polymer typepolypeptide
Formula Weight23976.4
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Chain B
DescriptionDNA mismatch repair protein mutL
Fragmentresidues in UNP 460-658
Polymer typepolypeptide
Formula Weight23976.4
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aA,Bpolypeptide(L)n/a
Natural/Genetically Modified Source
Scientific NameNeisseria gonorrhoeae
Source Genusn/a
GenemutL, NGO0744, NgoL
Host Common Namen/a
Host Scientific NameEscherichia coli
Host Genusn/a
Host Cell Linen/a
Host StrainBL21DE3pLysS
Host Vector TypePlasmid
Host Plasmidn/a
 
Crystallization Experiments
MethodVAPOR DIFFUSION, HANGING DROP
PH8.5
Temperature298.0
Details16% Peg8K, 0.2M magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
49.5062.1092.10
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.00104.6090.00
Space Group
P 1 21 1
Diffraction Detector
DetectorCCD
TypeMARMOSAIC 225 mm CCD
Detailsn/a
Collection Date2009-01-05
 
Diffraction Radiation
MonochromatorSi 111 CHANNEL
Diffraction ProtocolMAD
Wavelengthn/a
Wavelength List0.97871
 
Diffraction Source
SourceSYNCHROTRON
TypeESRF BEAMLINE BM14
SiteESRF
BeamlineBM14
 
Reflection Details
Observed Criterion Sigma (F)n/a
Observed Criterion Sigma (I)n/a
Resolution (High)2.40
Resolution (Low)50.00
Number Reflections (All) n/a
Number Reflections (Observed)19709
Percent Possible (Observed)98.2
R Merge I (Observed)0.041
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancy3.0
 
High Resolution Shell Details
Resolution(High)2.40
Resolution(Low)2.49
Percent Possible(All) 94.20
R Merge I(Observed)0.426
Mean I Over Sigma(Observed)2.1
R Sym I(Observed)n/a
Redundancy2.4
Num Unique Reflections(All)n/a
 
Refinement Statistics
Structure Solution MethodMAD
Resolution (High)2.40
Resolution (Low)44.44
Cut-off Sigma (F)n/a
Cut-off Sigma (I)n/a
Number of Reflections (All)n/a
Number of Reflections (Observed)18165
Number of Reflections (R-Free) 1543
Percent Reflections (Observed)92.29
R-Factor (All)n/a
R-Factor (Observed)0.22085
R-Work0.21649
R-Free0.27207
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value60.930
Anisotropic B[1][1]-0.36
Anisotropic B[1][2]0.00
Anisotropic B[1][3]-2.28
Anisotropic B[2][2]-1.28
Anisotropic B[2][3]0.00
Anisotropic B[3][3]0.49
 
Resolution Shells
Shell Resol (High)2.40
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)94
Number of Reflections (R-Work)1066
R-Factor (R-Work)0.383
R-Factor (R-Free)0.441
R-Free Errorn/a
Percent Reflections (Observed)74.50
 
RMS Deviations
First|Previous|1 of 4|Next|Last|
Parameter TypeDeviation From Ideal
r_bond_refined_d0.017
r_bond_other_dn/a
r_angle_refined_deg1.881
r_angle_other_degn/a
r_dihedral_angle_1_deg6.602
r_dihedral_angle_2_deg35.075
r_dihedral_angle_3_deg20.342
r_dihedral_angle_4_deg18.053
r_chiral_restr0.120
r_gen_planes_refined0.009
First|Previous|1 of 4|Next|Last|
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms2842
Nucleic Acid Atoms0
Heterogen Atoms0
Solvent Atoms108
 
Programs
Data CollectionMxCube
Data Reduction (intensity integration)HKL-2000
Data Reduction (data scaling)HKL-2000
Structure SolutionSHELXS
Structure RefinementREFMAC 5.5.0072
 
Software
Classificationdata collection
Software NameMxCube
 
Classificationmodel building
Software NameSHELXS
 
Classificationrefinement
Software NameREFMAC
Software Version 5.5.0072
 
Sequence Chain
A
Sequence
  1   TMGSSHHHHH  HSSGLVPRGS  HSQSELPPLG  FAIAQLLGIY  ILAQAEDSLL  LIDMHAAAER

 61   VNYEKMKRQR  QENGNLQSQH  LLIPVTFAAS  HEECAALADH  AETLAGFGLE  LSDMGGNTLA

121   VRAAPVMLGK  SDVVSLARDV  LGELAQVGSS  QTIASHENRI  LATMSCHGSI  RAGRRLTLPE

181   MNALLRDMEN  TPRSNQCNHG  RPTWVKLTLK  ELDTLFLRGQ    

Sequence Chain
B
Sequence
  1   TMGSSHHHHH  HSSGLVPRGS  HSQSELPPLG  FAIAQLLGIY  ILAQAEDSLL  LIDMHAAAER

 61   VNYEKMKRQR  QENGNLQSQH  LLIPVTFAAS  HEECAALADH  AETLAGFGLE  LSDMGGNTLA

121   VRAAPVMLGK  SDVVSLARDV  LGELAQVGSS  QTIASHENRI  LATMSCHGSI  RAGRRLTLPE

181   MNALLRDMEN  TPRSNQCNHG  RPTWVKLTLK  ELDTLFLRGQ