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PDB | 3G1A | Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with ...

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Internal ID
64025
PDB Entry ID
3G1A
Title
Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate
Authors
Fedorov, A.A.,Fedorov, E.V.,Chan, K.K.,Gerlt, J.A.,Almo, S.C.
Primary Citation
AuthorsChan, K.K., Wood, B.M., Fedorov, A.A., Fedorov, E.V., Imker, H.J., Amyes, T.L., Richard, J.P., Almo, S.C., Gerlt, J.A.
TitleMechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
JournalBiochemistry, v.48, pp.5518 - 5531, 2009
AbstractView
Pubmed19435314
DOI10.1021/bi900623r
 
History
Deposition: 2009-01-29Release: 2009-06-23Last Modified:
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
1.500.1890.1870.207P 1 21 1
Unit Cell
Length [Å]a59.73b64.14c61.52
Angles [°]alpha90.00beta115.36gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1Orotidine 5'-phosphate decarboxylaseR101PA, B4.1.1.23
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Methanothermobacter thermautotrophicus str. Delta HEscherichia coli
Related PDB Entries
Chemical Component
IdentifierNameFromulaLigand StructureLigand Interaction
UP66-AZA URIDINE 5'-MONOPHOSPHATEC8H12N3O9P[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordLYASE
Textorotidine 5'-monophosphate decarboxylase, 6-azaUMP, Decarboxylase, Pyrimidine biosynthesis, LYASE
 
Polymeric Molecules
Chain A
DescriptionOrotidine 5'-phosphate decarboxylase
MutationR101P
Polymer typepolypeptide
Formula Weight24884.8
Source Methodgenetically manipulated
Entity NameOMP decarboxylase, OMPDCase, OMPdecase
Entity Name Sysn/a
 
Chain B
DescriptionOrotidine 5'-phosphate decarboxylase
MutationR101P
Polymer typepolypeptide
Formula Weight24884.8
Source Methodgenetically manipulated
Entity NameOMP decarboxylase, OMPDCase, OMPdecase
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aA,Bpolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
UP66-AZA URIDINE 5'-MONOPHOSPHATEC8H12N3O9P325.171View
EC and Associated Pathways
ChainsIUBMBKEGG EnzymeMetaCycReactome
A, B4.1.1.234.1.1.234.1.1.234.1.1.23
Natural/Genetically Modified Source
Scientific NameMethanothermobacter thermautotrophicus str. Delta H
Source Genusn/a
GenepyrF, MTH_129
Host Common Namen/a
Host Scientific NameEscherichia coli
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Crystallization Experiments
MethodVAPOR DIFFUSION, HANGING DROP
PH8.5
Temperature293.0
DetailsPEG 3350, 0.1M tris, 0.2M magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
59.7364.1461.52
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.00115.3690.00
Space Group
P 1 21 1
Diffraction Detector
DetectorCCD
TypeADSC QUANTUM 4
Detailsn/a
Collection Date2007-10-19
 
Diffraction Radiation
MonochromatorSi 111 CHANNEL
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List0.97915
 
Diffraction Source
SourceSYNCHROTRON
TypeNSLS BEAMLINE X4A
SiteNSLS
BeamlineX4A
 
Reflection Details
Observed Criterion Sigma (F)0.0
Observed Criterion Sigma (I)0.0
Resolution (High)1.50
Resolution (Low)25.00
Number Reflections (All) 66146
Number Reflections (Observed)66146
Percent Possible (Observed)98.4
R Merge I (Observed)0.062
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancyn/a
 
Refinement Statistics
Structure Solution MethodMOLECULAR REPLACEMENT
Resolution (High)1.50
Resolution (Low)25.00
Cut-off Sigma (F)0.0
Cut-off Sigma (I)0.2
Number of Reflections (All)66146
Number of Reflections (Observed)66146
Number of Reflections (R-Free) 3370
Percent Reflections (Observed)98.40
R-Factor (All)0.189
R-Factor (Observed)0.189
R-Work0.187
R-Free0.207
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Valuen/a
Anisotropic B[1][1]n/a
Anisotropic B[1][2]n/a
Anisotropic B[1][3]n/a
Anisotropic B[2][2]n/a
Anisotropic B[2][3]n/a
Anisotropic B[3][3]n/a
 
RMS Deviations
Parameter TypeDeviation From Ideal
c_bond_d0.006
c_angle_deg1.38
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms3299
Nucleic Acid Atoms0
Heterogen Atoms42
Solvent Atoms336
 
Programs
Data CollectionADSC Quantum
Data Reduction (intensity integration)DENZO
Data Reduction (data scaling)SCALEPACK
Structure SolutionBALBES
Structure RefinementCNS 1.1
 
Software
Classificationdata collection
Software NameADSC
Software Version Quantum
 
Classificationmodel building
Software NameBALBES
 
Classificationrefinement
Software NameCNS
Software Version 1.1
 
Sequence Chain
A
Sequence
  1   MRSRRVDVMD  VMNRLILAMD  LMNRDDALRV  TGEVREYIDT  VKIGYPLVLS  EGMDIIAEFR

 61   KRFGCRIIAD  FKVADIPETN  EKICRATFKA  GADAIIVHGF  PGADSVRACL  NVAEEMGREV

121   FLLTEMSHPG  AEMFIQGAAD  EIARMGVDLG  VKNYVGPSTR  PERLSRLREI  IGQDSFLISP

181   GVGAQGGDPG  ETLRFADAII  VGRSIYLADN  PAAAAAGIIE  SIKDLLNP  

Sequence Chain
B
Sequence
  1   MRSRRVDVMD  VMNRLILAMD  LMNRDDALRV  TGEVREYIDT  VKIGYPLVLS  EGMDIIAEFR

 61   KRFGCRIIAD  FKVADIPETN  EKICRATFKA  GADAIIVHGF  PGADSVRACL  NVAEEMGREV

121   FLLTEMSHPG  AEMFIQGAAD  EIARMGVDLG  VKNYVGPSTR  PERLSRLREI  IGQDSFLISP

181   GVGAQGGDPG  ETLRFADAII  VGRSIYLADN  PAAAAAGIIE  SIKDLLNP