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

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Basic information

Entry
Database: PDB / ID: 3pby
TitleCrystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate
ComponentsOrotidine 5'-monophosphate decarboxylase
KeywordsLYASE / tim barrel / orotidine 5'-monophosphate decarboxylase / 6-azauridine 5'-monophosphate
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-AZA URIDINE 5'-MONOPHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanobacterium thermoautotrophicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Iiams, 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
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,4605
Polymers49,7172
Non-polymers7423
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-42 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.768, 64.046, 61.611
Angle α, β, γ (deg.)90.00, 115.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24858.617 Da / Num. of mol.: 2 / Mutation: R101P, L123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobacterium thermoautotrophicum (archaea)
Strain: Delta H / Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-UP6 / 6-AZA URIDINE 5'-MONOPHOSPHATE / 6-AZA-UMP


Mass: 325.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12N3O9P
#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.: 419 / 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: 42.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.1M Sodium cacodilate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K, temperature 293K

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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: Aug 7, 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: 1.3→32.376 Å / Num. all: 97097 / Num. obs: 97097 / % possible obs: 94.29 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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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: 3G18

3g18


Resolution: 1.3→32.376 Å / SU ML: 0.15 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1688 4858 5 %RANDOM
Rwork0.1602 ---
all0.1606 97097 --
obs0.1606 97097 94.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.706 Å2 / ksol: 0.402 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2492 Å2-0 Å2-2.0899 Å2
2--2.1495 Å2-0 Å2
3---0.0997 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 48 419 3778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063523
X-RAY DIFFRACTIONf_angle_d1.1254776
X-RAY DIFFRACTIONf_dihedral_angle_d15.751366
X-RAY DIFFRACTIONf_chiral_restr0.073539
X-RAY DIFFRACTIONf_plane_restr0.007635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.31490.23891060.22941828X-RAY DIFFRACTION57
1.3149-1.33030.265980.232073X-RAY DIFFRACTION63
1.3303-1.34660.23381220.22552220X-RAY DIFFRACTION69
1.3466-1.36360.23441290.21482409X-RAY DIFFRACTION74
1.3636-1.38150.23131390.20152588X-RAY DIFFRACTION81
1.3815-1.40050.2061280.19722897X-RAY DIFFRACTION88
1.4005-1.42050.20871640.19083176X-RAY DIFFRACTION98
1.4205-1.44170.1951840.17663240X-RAY DIFFRACTION100
1.4417-1.46420.2091780.16863260X-RAY DIFFRACTION100
1.4642-1.48820.16551520.16623249X-RAY DIFFRACTION100
1.4882-1.51390.19311620.15853239X-RAY DIFFRACTION100
1.5139-1.54140.19191640.163293X-RAY DIFFRACTION100
1.5414-1.57110.15252010.15593213X-RAY DIFFRACTION100
1.5711-1.60310.17331720.15283209X-RAY DIFFRACTION100
1.6031-1.6380.18081800.14443251X-RAY DIFFRACTION100
1.638-1.67610.15921600.1463279X-RAY DIFFRACTION100
1.6761-1.7180.16071830.14923255X-RAY DIFFRACTION100
1.718-1.76440.18711480.15093272X-RAY DIFFRACTION100
1.7644-1.81640.17641680.15063273X-RAY DIFFRACTION100
1.8164-1.8750.15511620.15123241X-RAY DIFFRACTION100
1.875-1.9420.15991500.1463302X-RAY DIFFRACTION100
1.942-2.01970.15051840.14623243X-RAY DIFFRACTION100
2.0197-2.11160.17341830.14743252X-RAY DIFFRACTION100
2.1116-2.22290.15331840.14633264X-RAY DIFFRACTION100
2.2229-2.36220.16051930.15043220X-RAY DIFFRACTION100
2.3622-2.54450.17591530.15173290X-RAY DIFFRACTION100
2.5445-2.80040.17941890.15713269X-RAY DIFFRACTION100
2.8004-3.20530.16111780.15633282X-RAY DIFFRACTION100
3.2053-4.03720.1311710.14093310X-RAY DIFFRACTION100
4.0372-32.38590.14261730.16253342X-RAY DIFFRACTION99

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