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PDB | 1T3P | Half-sandwich arene ruthenium(II)-enzyme complex

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Internal ID
22458
PDB Entry ID
1T3P
Title
Half-sandwich arene ruthenium(II)-enzyme complex
Authors
McNae, I.W.,Fishburne, K.,Habtemariam, A.,Hunter, T.M.,Melchart, M.,Wang, F.,Walkinshaw, M.D.,Sadler, P.J.
Primary Citation
AuthorsMcNae, I.W., Fishburne, K., Habtemariam, A., Hunter, T.M., Melchart, M., Wang, F., Walkinshaw, M.D., Sadler, P.J.
TitleHalf-sandwich arene ruthenium(II)-enzyme complex
JournalCHEM.COMMUN.(CAMB.), v.16, pp.1786 - 1787, 2004
AbstractView
Pubmed15306883
DOI10.1039/b408141b
 
History
Deposition: 2004-04-27Release: 2005-07-26Last Modified: 2009-02-24
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
1.600.1840.1820.217P 43 21 2
Unit Cell
Length [Å]a80.14b80.14c37.06
Angles [°]alpha90.00beta90.00gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1Lysozyme CA3.2.1.17
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Gallus galluschickenn/a
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
CLCHLORIDE IONCl1[View][View]
NASODIUM IONNa1[View][View]
ACTACETATE IONC2H3O21[View][View]
RU7PARA-CYMENE RUTHENIUM CHLORIDEC10H14Cl2Ru[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordHYDROLASE
Textruthenium, tetragonal lysozyme, HYDROLASE
 
Polymeric Molecules
Chain A
DescriptionLysozyme C
Polymer typepolypeptide
Formula Weight14331.2
Source Methodnatural source
Entity Name1,4-beta-N-acetylmuramidase C; Allergen Gal d 4; Gal d IV, egg white lysozyme
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aApolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
CLCHLORIDE IONCl135.453View
NASODIUM IONNa122.990View
ACTACETATE IONC2H3O2159.045View
RU7PARA-CYMENE RUTHENIUM CHLORIDEC10H14Cl2Ru306.197View
EC and Associated Pathways
ChainsIUBMBKEGG EnzymeMetaCycReactome
A3.2.1.173.2.1.173.2.1.173.2.1.17
Natural/Genetically Modified Source
Common Namechicken
Scientific NameGallus gallus
Source GenusGallus
Host Common Namen/a
Host Scientific Namen/a
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Crystallization Experiments
MethodVAPOR DIFFUSION, HANGING DROP
PH4.5
Temperature277.0
DetailsNaCl, Na acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
80.1480.1437.06
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.0090.00
Space Group
P 43 21 2
Diffraction Detector
DetectorCCD
TypeADSC QUANTUM 4
Detailsn/a
Collection Date2004-02-21
 
Diffraction Radiation
Monochromatorn/a
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List0.976
 
Diffraction Source
SourceSYNCHROTRON
TypeSRS BEAMLINE PX14.2
SiteSRS
BeamlinePX14.2
 
Reflection Details
Observed Criterion Sigma (F)2.4
Observed Criterion Sigma (I)2.4
Resolution (High)1.60
Resolution (Low)56.80
Number Reflections (All) n/a
Number Reflections (Observed)16497
Percent Possible (Observed)99.9
R Merge I (Observed)n/a
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plot17.6
Redundancy6.9
 
High Resolution Shell Details
Resolution(High)1.60
Resolution(Low)1.69
Percent Possible(All) 100.00
R Merge I(Observed)n/a
Mean I Over Sigma(Observed)2.4
R Sym I(Observed)0.315
Redundancy7.1
Num Unique Reflections(All)16705
 
Refinement Statistics
Structure Solution MethodMOLECULAR REPLACEMENT
Resolution (High)1.60
Resolution (Low)56.80
Cut-off Sigma (F)2.0
Cut-off Sigma (I)n/a
Number of Reflections (All)15623
Number of Reflections (Observed)15623
Number of Reflections (R-Free) 831
Percent Reflections (Observed)99.88
R-Factor (All)0.1841
R-Factor (Observed)0.1841
R-Work0.1823
R-Free0.21741
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value15.348
Anisotropic B[1][1]-0.40
Anisotropic B[1][2]0.00
Anisotropic B[1][3]0.00
Anisotropic B[2][2]-0.40
Anisotropic B[2][3]0.00
Anisotropic B[3][3]0.79
 
Resolution Shells
Shell Resol (High)1.60
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)66
Number of Reflections (R-Work)1121
R-Factor (R-Work)0.217
R-Factor (R-Free)0.263
R-Free Errorn/a
Percent Reflections (Observed)n/a
 
RMS Deviations
Parameter TypeDeviation From Ideal
r_bond_refined_d0.012
r_bond_other_d0.002
r_angle_refined_deg1.422
r_angle_other_deg1.507
r_dihedral_angle_1_deg6.336
r_chiral_restr0.089
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_nbd_refined0.260
r_nbd_other0.254
r_nbtor_other0.083
r_xyhbond_nbd_refined0.157
r_metal_ion_refined0.057
r_symmetry_vdw_refined0.066
r_symmetry_vdw_other0.320
r_symmetry_hbond_refined0.156
r_mcbond_it0.819
r_mcangle_it1.503
r_scbond_it2.323
r_scangle_it3.837
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms1001
Nucleic Acid Atoms0
Heterogen Atoms20
Solvent Atoms184
 
Programs
Data Collectionn/a
Data Reduction (intensity integration)MOSFLM
Data Reduction (data scaling)CCP4 (SCALA)
Structure SolutionMOLREP
Structure RefinementREFMAC 5.1.24
 
Software
Classificationrefinement
Software NameREFMAC
Software Version 5.1.24
 
Sequence Chain
A
Sequence
  1   KVFGRCELAA  AMKRHGLDNY  RGYSLGNWVC  AAKFESNFNT  QATNRNTDGS  TDYGILQINS

 61   RWWCNDGRTP  GSRNLCNIPC  SALLSSDITA  SVNCAKKIVS  DGNGMNAWVA  WRNRCKGTDV

121   QAWIRGCRL