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- PDB-3lv6: Crystal structure of the mutant I218F of orotidine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 3lv6
TitleCrystal structure of the mutant I218F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / mutant I218F / BMP / 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
6-HYDROXYURIDINE-5'-PHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 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
DepositionFeb 19, 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)50,5184
Polymers49,8372
Non-polymers6802
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-35 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.612, 63.211, 60.964
Angle α, β, γ (deg.)90.00, 114.82, 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: 24918.713 Da / Num. of mol.: 2 / Mutation: I218F
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-BMP / 6-HYDROXYURIDINE-5'-PHOSPHATE


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.: 352 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
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: Nov 11, 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: 1.45→32.468 Å / Num. all: 65670 / Num. obs: 65670 / % possible obs: 90.33 % / 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: 1.451→32.468 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 3332 5.07 %RANDOM
Rwork0.1633 ---
all0.1643 65670 --
obs0.1643 65670 90.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.573 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 1.451→32.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 44 352 3701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083401
X-RAY DIFFRACTIONf_angle_d1.1674596
X-RAY DIFFRACTIONf_dihedral_angle_d16.2151318
X-RAY DIFFRACTIONf_chiral_restr0.095524
X-RAY DIFFRACTIONf_plane_restr0.007603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.451-1.47160.2021680.17441396X-RAY DIFFRACTION49
1.4716-1.49350.2117820.18891559X-RAY DIFFRACTION54
1.4935-1.51690.1966870.17461719X-RAY DIFFRACTION60
1.5169-1.54170.2186980.1751882X-RAY DIFFRACTION66
1.5417-1.56830.19221120.17132119X-RAY DIFFRACTION74
1.5683-1.59680.1811390.16082480X-RAY DIFFRACTION87
1.5968-1.62760.19161400.1612795X-RAY DIFFRACTION97
1.6276-1.66080.18431550.15832783X-RAY DIFFRACTION98
1.6608-1.69690.17851560.15582797X-RAY DIFFRACTION98
1.6969-1.73640.18981340.15062839X-RAY DIFFRACTION98
1.7364-1.77980.16341500.15682804X-RAY DIFFRACTION98
1.7798-1.82790.17711600.15652792X-RAY DIFFRACTION98
1.8279-1.88170.18251600.16042828X-RAY DIFFRACTION98
1.8817-1.94240.20111530.15992813X-RAY DIFFRACTION99
1.9424-2.01180.16381490.15882841X-RAY DIFFRACTION99
2.0118-2.09240.17111580.15992862X-RAY DIFFRACTION99
2.0924-2.18760.18161620.15952817X-RAY DIFFRACTION99
2.1876-2.30290.16451510.15982848X-RAY DIFFRACTION99
2.3029-2.44710.19631690.16942851X-RAY DIFFRACTION99
2.4471-2.6360.2121570.17152867X-RAY DIFFRACTION99
2.636-2.90110.2151390.17612900X-RAY DIFFRACTION100
2.9011-3.32050.17391360.17152906X-RAY DIFFRACTION100
3.3205-4.18210.15071470.1452921X-RAY DIFFRACTION100
4.1821-32.47570.17371700.15492919X-RAY DIFFRACTION99

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