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- PDB-3m44: Crystal structure of the mutant V201A of orotidine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 3m44
TitleCrystal structure of the mutant V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / orotidine 5'-monophosphate decarboxylase / mutant V201A
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
Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2010
Title: Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.
Authors: Wood, B.M. / Amyes, T.L. / Fedorov, A.A. / Fedorov, E.V. / Shabila, A. / Almo, S.C. / Richard, J.P. / Gerlt, J.A.
History
DepositionMar 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)49,8053
Polymers49,7132
Non-polymers921
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-31 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.806, 56.787, 125.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24856.645 Da / Num. of mol.: 2 / Mutation: V201A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4M sodium malonate, pH 7.0, 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: Sep 4, 2009
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: 1.4→33.76 Å / Num. all: 73236 / Num. obs: 73236 / % possible obs: 90.34 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069

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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: 1.4→33.76 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 3692 5.04 %RANDOM
Rwork0.2126 ---
all0.214 73236 --
obs0.214 73236 90.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.914 Å2 / ksol: 0.436 e/Å3
Refinement stepCycle: LAST / Resolution: 1.4→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 6 240 3429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063289
X-RAY DIFFRACTIONf_angle_d1.0124445
X-RAY DIFFRACTIONf_dihedral_angle_d13.4051239
X-RAY DIFFRACTIONf_chiral_restr0.073510
X-RAY DIFFRACTIONf_plane_restr0.006587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4180.3794790.32441391X-RAY DIFFRACTION48
1.418-1.43740.2632850.31041619X-RAY DIFFRACTION56
1.4374-1.45790.3274750.29831763X-RAY DIFFRACTION59
1.4579-1.47970.2881940.28661880X-RAY DIFFRACTION65
1.4797-1.50280.34421140.28232099X-RAY DIFFRACTION70
1.5028-1.52750.2851190.25132216X-RAY DIFFRACTION77
1.5275-1.55380.29571490.24842442X-RAY DIFFRACTION84
1.5538-1.58210.27521280.23962713X-RAY DIFFRACTION92
1.5821-1.61250.22231530.22582911X-RAY DIFFRACTION99
1.6125-1.64540.24461370.23462908X-RAY DIFFRACTION100
1.6454-1.68120.29771430.22612951X-RAY DIFFRACTION99
1.6812-1.72030.2311500.21782937X-RAY DIFFRACTION100
1.7203-1.76330.2531530.21932913X-RAY DIFFRACTION100
1.7633-1.8110.27341630.22322906X-RAY DIFFRACTION100
1.811-1.86430.27711400.2062983X-RAY DIFFRACTION100
1.8643-1.92440.21641650.21392934X-RAY DIFFRACTION100
1.9244-1.99320.22521680.1982921X-RAY DIFFRACTION100
1.9932-2.0730.23081620.22947X-RAY DIFFRACTION100
2.073-2.16730.21861370.19862998X-RAY DIFFRACTION100
2.1673-2.28160.21021780.19172937X-RAY DIFFRACTION100
2.2816-2.42450.23521640.20982976X-RAY DIFFRACTION100
2.4245-2.61160.21641640.20662999X-RAY DIFFRACTION100
2.6116-2.87430.22111500.20782999X-RAY DIFFRACTION100
2.8743-3.28990.23991800.20972987X-RAY DIFFRACTION100
3.2899-4.14370.21381710.18453053X-RAY DIFFRACTION100
4.1437-33.77040.24391710.21233161X-RAY DIFFRACTION99

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