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- PDB-3pc0: Crystal structure of the mutant V155S of orotidine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 3pc0
TitleCrystal structure of the mutant V155S 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: 1.298 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)50,4885
Polymers49,7452
Non-polymers7423
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-43 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.707, 63.831, 61.696
Angle α, β, γ (deg.)90.00, 115.22, 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: 24872.645 Da / Num. of mol.: 2 / Mutation: R101P, V155S
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.: 398 / 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: 42.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 5000, 0.1M MES, 0.2M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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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: 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: 1.298→32.506 Å / Num. all: 92336 / Num. obs: 92336 / % possible obs: 89.4 % / 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: 1.298→32.506 Å / SU ML: 0.15 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 4620 5 %RANDOM
Rwork0.1756 ---
all0.1765 92336 --
obs0.1765 92336 89.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.259 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8507 Å2-0 Å2-2.2666 Å2
2--4.502 Å2-0 Å2
3----0.6514 Å2
Refinement stepCycle: LAST / Resolution: 1.298→32.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 48 398 3759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063511
X-RAY DIFFRACTIONf_angle_d1.0824759
X-RAY DIFFRACTIONf_dihedral_angle_d15.9431362
X-RAY DIFFRACTIONf_chiral_restr0.073539
X-RAY DIFFRACTIONf_plane_restr0.007630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2985-1.31330.3668850.33151218X-RAY DIFFRACTION38
1.3133-1.32870.2902780.3061459X-RAY DIFFRACTION45
1.3287-1.34490.2994780.29131700X-RAY DIFFRACTION52
1.3449-1.36190.3736790.28011881X-RAY DIFFRACTION57
1.3619-1.37990.31151200.25552113X-RAY DIFFRACTION65
1.3799-1.39880.29511210.2482337X-RAY DIFFRACTION72
1.3988-1.41870.27551320.23732615X-RAY DIFFRACTION79
1.4187-1.43990.23151510.22312739X-RAY DIFFRACTION85
1.4399-1.46240.25411620.20922990X-RAY DIFFRACTION92
1.4624-1.48640.25691560.1993161X-RAY DIFFRACTION96
1.4864-1.5120.20181740.18853246X-RAY DIFFRACTION100
1.512-1.53950.19081630.18913269X-RAY DIFFRACTION100
1.5395-1.56910.23111780.17883239X-RAY DIFFRACTION100
1.5691-1.60120.18581790.18053258X-RAY DIFFRACTION100
1.6012-1.6360.19651880.17173249X-RAY DIFFRACTION100
1.636-1.6740.20651580.1743289X-RAY DIFFRACTION100
1.674-1.71590.19031930.17343271X-RAY DIFFRACTION100
1.7159-1.76230.1861770.17683233X-RAY DIFFRACTION100
1.7623-1.81410.20161730.17453286X-RAY DIFFRACTION100
1.8141-1.87270.19561840.17123227X-RAY DIFFRACTION100
1.8727-1.93960.19341880.16863279X-RAY DIFFRACTION100
1.9396-2.01720.19431620.16333251X-RAY DIFFRACTION100
2.0172-2.1090.17941690.16543298X-RAY DIFFRACTION100
2.109-2.22020.19431700.16443273X-RAY DIFFRACTION100
2.2202-2.35930.17821720.16263266X-RAY DIFFRACTION100
2.3593-2.54140.17821550.16293299X-RAY DIFFRACTION100
2.5414-2.7970.19381830.17413278X-RAY DIFFRACTION100
2.797-3.20140.21121760.17643297X-RAY DIFFRACTION100
3.2014-4.03230.15241750.14723320X-RAY DIFFRACTION100
4.0323-32.51620.16331410.16353375X-RAY DIFFRACTION99

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