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- PDB-3w07: Atomic resolution structure of orotidine 5'-monophosphate decarbo... -

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Basic information

Entry
Database: PDB / ID: 3w07
TitleAtomic resolution structure of orotidine 5'-monophosphate decarboxylase from Methanothermobacter thermoautotrophicus bound with UMP.
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / Orotidine 5'-monophosphate decarboxylase
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
URIDINE-5'-MONOPHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.03 Å
AuthorsFujihashi, M. / Pai, E.F. / Miki, K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Atomic resolution structure of the orotidine 5'-monophosphate decarboxylase product complex combined with surface plasmon resonance analysis: implications for the catalytic mechanism.
Authors: Fujihashi, M. / Mito, K. / Pai, E.F. / Miki, K.
History
DepositionOct 22, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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)27,7963
Polymers27,3791
Non-polymers4162
Water3,027168
1
A: Orotidine 5'-phosphate decarboxylase
hetero molecules

A: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5916
Polymers54,7592
Non-polymers8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5100 Å2
ΔGint-41 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.943, 103.233, 73.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

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Components

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


Mass: 27379.402 Da / Num. of mol.: 1 / Mutation: R101P
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 / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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. THERMOAUTOTROPHICUM 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: 2.03 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.28M sodium citrate, 5%(v/v) dioxane, 0.1M HEPES-Na pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2003
RadiationMonochromator: default / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.03→50 Å / Num. obs: 108363 / % possible obs: 99.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 46.3
Reflection shellResolution: 1.03→1.04 Å / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1.8 / % possible all: 97.1

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.03→10 Å / Num. parameters: 19192 / Num. restraintsaints: 28126 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1386 --RANDOM
Rwork0.1177 ---
all-108363 --
obs-102765 93.8 %-
Refine analyzeNum. disordered residues: 72 / Occupancy sum hydrogen: 688 / Occupancy sum non hydrogen: 1777.15
Refinement stepCycle: LAST / Resolution: 1.03→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 27 168 1807
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.038
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.045
X-RAY DIFFRACTIONs_approx_iso_adps0.109

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