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- PDB-3nqf: Crystal structure of the mutant L123S of orotidine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 3nqf
TitleCrystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE/LYASE INHIBITOR / orotidine 5'-monophosphate decarboxylase / Methanobacterium thermoautotrophicum / inhibitor BMP / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol
Similarity search - Function
: / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel ...: / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-HYDROXYURIDINE-5'-PHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.312 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2011
Title: Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site.
Authors: Iiams, V. / Desai, B.J. / Fedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Gerlt, J.A.
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Nov 2, 2011Group: Database references
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orotidine 5'-phosphate decarboxylase
B: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4905
Polymers49,7172
Non-polymers7723
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-43 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.854, 63.934, 61.738
Angle α, β, γ (deg.)90.00, 115.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Orotidine 5'-phosphate decarboxylase / OMP decarboxylase / OMPDCase / OMPdecase


Mass: 24858.617 Da / Num. of mol.: 2 / Mutation: L123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-BMP / 6-HYDROXYURIDINE-5'-PHOSPHATE


Type: RNA linking / Mass: 340.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O10P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 0.1M Bis-Tris, 0.2M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.312→30.736 Å / Num. all: 95704 / Num. obs: 95704 / % possible obs: 95.51 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.089

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3G18

3g18


Resolution: 1.312→30.736 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 16.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1773 4799 5.01 %
Rwork0.1653 --
obs0.1659 95704 95.51 %
all-95704 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.907 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3507 Å2-0 Å2-1.9746 Å2
2--2.4886 Å2-0 Å2
3----0.1379 Å2
Refinement stepCycle: LAST / Resolution: 1.312→30.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 50 468 3829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063524
X-RAY DIFFRACTIONf_angle_d1.1194775
X-RAY DIFFRACTIONf_dihedral_angle_d15.7421374
X-RAY DIFFRACTIONf_chiral_restr0.073538
X-RAY DIFFRACTIONf_plane_restr0.006633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3125-1.32740.23741300.24262368X-RAY DIFFRACTION75
1.3274-1.3430.25821190.23392640X-RAY DIFFRACTION84
1.343-1.35940.23061480.22642800X-RAY DIFFRACTION89
1.3594-1.37660.23571590.21742904X-RAY DIFFRACTION92
1.3766-1.39470.2251390.20512942X-RAY DIFFRACTION93
1.3947-1.41380.23761530.20332980X-RAY DIFFRACTION94
1.4138-1.4340.21791680.18862999X-RAY DIFFRACTION95
1.434-1.45540.22181440.17742998X-RAY DIFFRACTION95
1.4554-1.47820.17431630.16783053X-RAY DIFFRACTION96
1.4782-1.50240.18491650.16392994X-RAY DIFFRACTION96
1.5024-1.52830.19171760.15943035X-RAY DIFFRACTION96
1.5283-1.55610.17891640.15963011X-RAY DIFFRACTION96
1.5561-1.5860.17511520.15723106X-RAY DIFFRACTION97
1.586-1.61840.16421640.15283057X-RAY DIFFRACTION96
1.6184-1.65360.17291670.1513023X-RAY DIFFRACTION97
1.6536-1.69210.1481750.14463039X-RAY DIFFRACTION97
1.6921-1.73440.13481630.14443077X-RAY DIFFRACTION97
1.7344-1.78130.16591800.15093103X-RAY DIFFRACTION97
1.7813-1.83370.18021680.15283069X-RAY DIFFRACTION98
1.8337-1.89290.1691660.14933121X-RAY DIFFRACTION98
1.8929-1.96050.16341300.14183129X-RAY DIFFRACTION98
1.9605-2.0390.16481630.14863123X-RAY DIFFRACTION98
2.039-2.13180.15331710.14913134X-RAY DIFFRACTION98
2.1318-2.24410.16911860.15193110X-RAY DIFFRACTION99
2.2441-2.38470.18791600.1543136X-RAY DIFFRACTION99
2.3847-2.56870.16381690.15663172X-RAY DIFFRACTION99
2.5687-2.8270.16271460.1643192X-RAY DIFFRACTION99
2.827-3.23570.1741850.16313166X-RAY DIFFRACTION100
3.2357-4.07520.14691730.14353196X-RAY DIFFRACTION100
4.0752-30.7440.15091530.15673228X-RAY DIFFRACTION98

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