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- PDB-3wk0: Wild-type orotidine 5'-monophosphate decarboxylase from M. thermo... -

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Basic information

Entry
Database: PDB / ID: 3wk0
TitleWild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate methyl ester
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / protein-ligand complex / TIM barrel / 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-O7M / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.41 Å
AuthorsFujihashi, M. / Pai, E.F. / Miki, K.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase.
Authors: Fujihashi, M. / Ishida, T. / Kuroda, S. / Kotra, L.P. / Pai, E.F. / Miki, K.
History
DepositionOct 17, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Assembly

Deposited unit
A: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9464
Polymers27,3791
Non-polymers5663
Water2,594144
1
A: Orotidine 5'-phosphate decarboxylase
hetero molecules

A: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8928
Polymers54,7592
Non-polymers1,1336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area4100 Å2
ΔGint-38 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.032, 103.562, 73.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 27379.402 Da / Num. of mol.: 1 / Mutation: L226R, N227I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: pyrF, MTH_129 / Plasmid: ?pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-O7M / 6-(methoxycarbonyl)uridine 5'-(dihydrogen phosphate)


Mass: 382.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O11P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. ...ACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. DEPOSITORS SEQUENCED THE GENOME FROM M. THERMOAUTOTROPHICUS AND CONFIRMED IT IS PRO.

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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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: Sodium citrate, pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9797 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: Default / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.41→100 Å / Num. obs: 43044 / % possible obs: 99.6 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 45.6
Reflection shellResolution: 1.41→1.43 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 6.5 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0066refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3WJY

3wjy


Resolution: 1.41→51.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.645 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2146 5 %RANDOM
Rwork0.169 ---
obs0.17 42886 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.79 Å2 / Biso mean: 14.5118 Å2 / Biso min: 2.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.83 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.41→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 37 144 1811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221879
X-RAY DIFFRACTIONr_angle_refined_deg1.8092.0012557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2723.65982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64915328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4991518
X-RAY DIFFRACTIONr_chiral_restr0.1130.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211449
X-RAY DIFFRACTIONr_mcbond_it0.9851.51179
X-RAY DIFFRACTIONr_mcangle_it1.66821914
X-RAY DIFFRACTIONr_scbond_it3.0773700
X-RAY DIFFRACTIONr_scangle_it4.9514.5642
LS refinement shellResolution: 1.41→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 146 -
Rwork0.208 2971 -
all-3117 -
obs--99.2 %
Refinement TLS params.Method: refined / Origin x: 18.7496 Å / Origin y: 40.4986 Å / Origin z: 29.5749 Å
111213212223313233
T0.0272 Å20.001 Å2-0.0014 Å2-0.0179 Å2-0.0056 Å2--0.0195 Å2
L0.2052 °2-0.0206 °20.0103 °2-0.4508 °2-0.1268 °2--0.2603 °2
S0.0128 Å °0.0204 Å °-0.0576 Å °-0.0735 Å °0.0087 Å °0.0022 Å °0.0496 Å °-0.0017 Å °-0.0215 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 225
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A302 - 303
4X-RAY DIFFRACTION1A401 - 544

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