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- PDB-1lol: Crystal structure of orotidine monophosphate decarboxylase comple... -

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Basic information

Entry
Database: PDB / ID: 1lol
TitleCrystal structure of orotidine monophosphate decarboxylase complex with XMP
Componentsorotidine 5'-monophosphate decarboxylase
KeywordsLYASE / TIM barrel
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
1,3-BUTANEDIOL / XANTHOSINE-5'-MONOPHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWu, N. / Pai, E.F.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5'-monophosphate decarboxylase.
Authors: Wu, N. / Pai, E.F.
History
DepositionMay 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Remark 999 sequence Author states that although residues 1 and 1001 are MET and residues 101 and 1101 are Arg ... sequence Author states that although residues 1 and 1001 are MET and residues 101 and 1101 are Arg according to the SwissProt entry, residues 1 and 1001 were LEU and residues 101 and 1101 were Pro in the original construct cloned of MT genomic dna.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: orotidine 5'-monophosphate decarboxylase
B: orotidine 5'-monophosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9006
Polymers49,9902
Non-polymers9114
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-31 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.570, 55.482, 66.129
Angle α, β, γ (deg.)90.00, 94.28, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biologically functional unit is a dimer composed of the two monomers in the asymmetric unit.

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Components

#1: Protein orotidine 5'-monophosphate decarboxylase / OMP DECARBOXYLASE / OMPDCASE / OMPDECASE


Mass: 24994.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Species: Methanothermobacter thermautotrophicus / Strain: delta H / Plasmid: pET15b / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE


Mass: 365.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: trisodium citrate, (+/-)1,3-butanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 8.5 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.2 Mtrisodium citrate1reservoirpH6.5-8.5
210 %(v/v)(+-)-1,3-butanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 33017 / Num. obs: 32685 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.2 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 100 Å / % possible obs: 99 % / Num. measured all: 376089 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.312

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Processing

Software
NameVersionClassification
EPMRphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.07 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 679650.23 / Data cutoff high rms absF: 679650.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1583 4.9 %RANDOM
Rwork0.193 ---
all0.193 33017 --
obs0.193 32092 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.0244 Å2 / ksol: 0.394803 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.19 Å20 Å23.48 Å2
2---3.85 Å20 Å2
3----3.34 Å2
Refine analyzeLuzzati coordinate error free: 0.25 Å / Luzzati sigma a free: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 60 180 3432
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it2.482
X-RAY DIFFRACTIONc_scangle_it3.72.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 279 5.3 %
Rwork0.234 4989 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3XMP.PARAMXMP.TOP
X-RAY DIFFRACTION4DIO.PARAMDIO.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Rfactor all: 0.193 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.234

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