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- PDB-3lht: Crystal structure of the mutant V201F of orotidine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 3lht
TitleCrystal structure of the mutant V201F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / mutant V201F / 6-hydroxyuridine-5'-phosphate / Decarboxylase / Pyrimidine biosynthesis
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
Chem-BMQ / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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
DepositionJan 23, 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 13, 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)50,5464
Polymers49,8652
Non-polymers6802
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-32 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.891, 64.365, 61.760
Angle α, β, γ (deg.)90.00, 115.44, 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: 24932.740 Da / Num. of mol.: 2 / Mutation: V201F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-BMQ / 1-(5'-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC ACID


Type: RNA linking / Mass: 340.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 0.1M Tris, 0.2M magnesium chloride, pH 8.5, 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: Jul 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.35→32.475 Å / Num. all: 85472 / Num. obs: 85472 / % possible obs: 91.78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063

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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: 1.35→32.475 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 4277 5 %RANDOM
Rwork0.2117 ---
all0.2127 85472 --
obs0.2127 85472 91.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.956 Å2 / ksol: 0.392 e/Å3
Refinement stepCycle: LAST / Resolution: 1.35→32.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 44 377 3728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073403
X-RAY DIFFRACTIONf_angle_d1.1374598
X-RAY DIFFRACTIONf_dihedral_angle_d15.8091320
X-RAY DIFFRACTIONf_chiral_restr0.084524
X-RAY DIFFRACTIONf_plane_restr0.006603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36440.3319800.29881443X-RAY DIFFRACTION50
1.3644-1.38040.32021020.2971639X-RAY DIFFRACTION57
1.3804-1.39730.3362870.28221812X-RAY DIFFRACTION61
1.3973-1.41490.34081140.28181955X-RAY DIFFRACTION67
1.4149-1.43360.31131140.25982130X-RAY DIFFRACTION72
1.4336-1.45320.24781300.26122225X-RAY DIFFRACTION78
1.4532-1.4740.27291330.25242465X-RAY DIFFRACTION84
1.474-1.4960.27661260.23822645X-RAY DIFFRACTION89
1.496-1.51930.28681660.22322814X-RAY DIFFRACTION97
1.5193-1.54430.24261520.22562973X-RAY DIFFRACTION100
1.5443-1.57090.2581320.2212975X-RAY DIFFRACTION100
1.5709-1.59940.2421440.21472916X-RAY DIFFRACTION100
1.5994-1.63020.24441630.22062951X-RAY DIFFRACTION100
1.6302-1.66350.24261320.2172966X-RAY DIFFRACTION100
1.6635-1.69960.25461400.21822932X-RAY DIFFRACTION100
1.6996-1.73920.25411650.21362922X-RAY DIFFRACTION100
1.7392-1.78270.24521580.20632961X-RAY DIFFRACTION100
1.7827-1.83090.23141670.19832952X-RAY DIFFRACTION100
1.8309-1.88470.22111590.20142894X-RAY DIFFRACTION100
1.8847-1.94560.22141700.19822956X-RAY DIFFRACTION100
1.9456-2.01510.25171510.1932949X-RAY DIFFRACTION100
2.0151-2.09580.21111640.20082927X-RAY DIFFRACTION100
2.0958-2.19110.22011390.19942977X-RAY DIFFRACTION100
2.1911-2.30660.21421570.20122973X-RAY DIFFRACTION100
2.3066-2.45110.20871530.20772923X-RAY DIFFRACTION100
2.4511-2.64030.25421470.21772963X-RAY DIFFRACTION100
2.6403-2.90580.23721740.22662959X-RAY DIFFRACTION100
2.9058-3.32590.23411580.22362984X-RAY DIFFRACTION100
3.3259-4.18890.19811420.19022992X-RAY DIFFRACTION100
4.1889-32.48450.19441580.18553022X-RAY DIFFRACTION99

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