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- PDB-4fx6: Crystal structure of the mutant V182A.R203A of orotidine 5'-monop... -

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Basic information

Entry
Database: PDB / ID: 4fx6
TitleCrystal structure of the mutant V182A.R203A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE/LYASE INHIBITOR / tim barrel / 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: 1.531 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
DepositionJul 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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
M: Orotidine 5'-phosphate decarboxylase
N: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5908
Polymers49,5412
Non-polymers1,0496
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-50 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.084, 66.404, 59.552
Angle α, β, γ (deg.)90.00, 101.85, 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: 24770.529 Da / Num. of mol.: 2 / Mutation: V182A, R203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.0 Sodium citrate, 0.1M cacodylate, 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: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.531→44.38 Å / Num. all: 62002 / Num. obs: 62002 / % possible obs: 97.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LTP

3ltp


Resolution: 1.531→44.38 Å / SU ML: 0.11 / σ(F): 1.35 / Phase error: 16.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 3157 5.09 %RANDOM
Rwork0.146 ---
obs0.1473 62002 97.99 %-
all-62002 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.531→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 68 373 3799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063630
X-RAY DIFFRACTIONf_angle_d1.1114924
X-RAY DIFFRACTIONf_dihedral_angle_d12.4651430
X-RAY DIFFRACTIONf_chiral_restr0.076551
X-RAY DIFFRACTIONf_plane_restr0.007656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.531-1.55390.20611160.19032330X-RAY DIFFRACTION91
1.5539-1.57820.1861290.17132575X-RAY DIFFRACTION98
1.5782-1.6040.17791380.16092553X-RAY DIFFRACTION98
1.604-1.63170.19511240.15752545X-RAY DIFFRACTION98
1.6317-1.66140.19951600.16452540X-RAY DIFFRACTION97
1.6614-1.69330.22611240.15622525X-RAY DIFFRACTION97
1.6933-1.72790.19691320.1552526X-RAY DIFFRACTION98
1.7279-1.76550.17851380.14492541X-RAY DIFFRACTION98
1.7655-1.80650.17631210.14812541X-RAY DIFFRACTION97
1.8065-1.85170.1791260.14392564X-RAY DIFFRACTION97
1.8517-1.90180.1891620.15042493X-RAY DIFFRACTION97
1.9018-1.95770.17661310.14842553X-RAY DIFFRACTION98
1.9577-2.02090.17361400.13852558X-RAY DIFFRACTION98
2.0209-2.09320.16461300.14412544X-RAY DIFFRACTION98
2.0932-2.1770.15171370.13792574X-RAY DIFFRACTION99
2.177-2.2760.18151400.13982599X-RAY DIFFRACTION99
2.276-2.3960.16211500.14632588X-RAY DIFFRACTION99
2.396-2.54610.16871580.15022569X-RAY DIFFRACTION100
2.5461-2.74270.18991420.15682614X-RAY DIFFRACTION100
2.7427-3.01870.17111550.15572617X-RAY DIFFRACTION100
3.0187-3.45530.15891410.14212625X-RAY DIFFRACTION100
3.4553-4.35270.15071180.12252638X-RAY DIFFRACTION100
4.3527-44.39840.16431450.14982633X-RAY DIFFRACTION97

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