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

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Basic information

Entry
Database: PDB / ID: 3wjx
TitleWild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with 6-amino-UMP
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
6-AMINOURIDINE 5'-MONOPHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.23 Å
AuthorsFujihashi, M. / Kuroda, S. / 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)27,9034
Polymers27,3791
Non-polymers5233
Water3,477193
1
A: Orotidine 5'-phosphate decarboxylase
hetero molecules

A: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8068
Polymers54,7592
Non-polymers1,0476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5410 Å2
ΔGint-48 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.885, 103.351, 73.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

21A-513-

HOH

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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-NUP / 6-AMINOURIDINE 5'-MONOPHOSPHATE


Mass: 339.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O9P
#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.: 193 / 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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: Sodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. obs: 64324 / % possible obs: 100 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.8
Reflection shellResolution: 1.23→1.25 Å / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 7 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3WK3

3wk3


Resolution: 1.23→29.99 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.04 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1636 3197 5 %RANDOM
Rwork0.156 ---
obs0.1564 64295 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.32 Å2 / Biso mean: 13.4658 Å2 / Biso min: 5.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2---0.25 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.23→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 34 193 1857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192017
X-RAY DIFFRACTIONr_angle_refined_deg1.4752.0022756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6325270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60422.68893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10715356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.021526
X-RAY DIFFRACTIONr_chiral_restr0.090.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0231586
LS refinement shellResolution: 1.229→1.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 236 -
Rwork0.167 4396 -
all-4632 -
obs--97.45 %
Refinement TLS params.Method: refined / Origin x: 18.6827 Å / Origin y: 40.1894 Å / Origin z: 29.8057 Å
111213212223313233
T0.0316 Å20.0002 Å2-0.0079 Å2-0.0031 Å2-0.0041 Å2--0.0099 Å2
L0.3856 °2-0.0127 °20.0056 °2-0.5961 °2-0.1474 °2--0.416 °2
S0.0119 Å °0.0324 Å °-0.0518 Å °-0.0913 Å °0.0071 Å °0.0054 Å °0.0849 Å °-0.0036 Å °-0.019 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 225
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A401 - 593

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