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- PDB-3qf0: Crystal structure of the mutant T159V,Y206F of orotidine 5'-monop... -

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Basic information

Entry
Database: PDB / ID: 3qf0
TitleCrystal structure of the mutant T159V,Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE/LYASE INHIBITOR / (beta-alpha)8 barrel / orotidine 5'-monophosphate decarboxylase / 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 str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2012
Title: Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.
Authors: Desai, B.J. / Wood, B.M. / Fedorov, A.A. / Fedorov, E.V. / Goryanova, B. / Amyes, T.L. / Richard, J.P. / Almo, S.C. / Gerlt, J.A.
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 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'-phosphate decarboxylase
B: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5065
Polymers49,7332
Non-polymers7723
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-44 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.930, 63.675, 61.432
Angle α, β, γ (deg.)90.00, 115.34, 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: 24866.725 Da / Num. of mol.: 2 / Mutation: T159V,Y206F
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-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.: 367 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M sodium citrate, 0.1M Hepes, pH 7.5, 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: Dec 5, 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: 1.34→32.446 Å / Num. all: 87118 / Num. obs: 87118 / % possible obs: 93.02 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LTP

3ltp


Resolution: 1.34→32.446 Å / SU ML: 0.13 / σ(F): 0 / σ(I): 0 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1923 4364 5.01 %RANDOM
Rwork0.1731 ---
all0.1741 87118 --
obs0.1741 87118 93.02 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.044 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5389 Å2-0 Å2-3.2815 Å2
2--3.1622 Å2-0 Å2
3----0.6233 Å2
Refinement stepCycle: LAST / Resolution: 1.34→32.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 50 367 3738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063592
X-RAY DIFFRACTIONf_angle_d1.0324877
X-RAY DIFFRACTIONf_dihedral_angle_d11.8381412
X-RAY DIFFRACTIONf_chiral_restr0.072549
X-RAY DIFFRACTIONf_plane_restr0.006652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.35520.4077650.32531313X-RAY DIFFRACTION44
1.3552-1.37120.3156630.31431568X-RAY DIFFRACTION53
1.3712-1.38790.3477900.31191842X-RAY DIFFRACTION62
1.3879-1.40550.34151040.28882103X-RAY DIFFRACTION72
1.4055-1.4240.34121270.26762437X-RAY DIFFRACTION82
1.424-1.44350.29361400.25682642X-RAY DIFFRACTION89
1.4435-1.46410.25551420.24412791X-RAY DIFFRACTION95
1.4641-1.48590.27311320.23092884X-RAY DIFFRACTION98
1.4859-1.50920.20661670.21452953X-RAY DIFFRACTION99
1.5092-1.53390.26891580.20932949X-RAY DIFFRACTION100
1.5339-1.56040.2161640.19692918X-RAY DIFFRACTION100
1.5604-1.58870.21681730.18542965X-RAY DIFFRACTION100
1.5887-1.61930.20411430.17832962X-RAY DIFFRACTION100
1.6193-1.65230.17891580.17742960X-RAY DIFFRACTION100
1.6523-1.68830.20861500.17922939X-RAY DIFFRACTION100
1.6883-1.72750.21131620.17152929X-RAY DIFFRACTION100
1.7275-1.77070.22081810.17252963X-RAY DIFFRACTION100
1.7707-1.81860.20751610.17132978X-RAY DIFFRACTION100
1.8186-1.87210.18971670.17062902X-RAY DIFFRACTION100
1.8721-1.93250.18621370.17282997X-RAY DIFFRACTION100
1.9325-2.00160.18991610.17152945X-RAY DIFFRACTION100
2.0016-2.08170.20261600.17072950X-RAY DIFFRACTION100
2.0817-2.17640.19451590.17852984X-RAY DIFFRACTION100
2.1764-2.29120.17781620.16732951X-RAY DIFFRACTION100
2.2912-2.43470.18841650.1672961X-RAY DIFFRACTION100
2.4347-2.62260.1981530.16772976X-RAY DIFFRACTION100
2.6226-2.88630.20671580.1782977X-RAY DIFFRACTION100
2.8863-3.30370.17991380.16433003X-RAY DIFFRACTION100
3.3037-4.16090.14851620.13973002X-RAY DIFFRACTION100
4.1609-32.45540.15941620.15333010X-RAY DIFFRACTION98

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