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- PDB-1lor: crystal structure of orotidine 5'-monophosphate complexed with BMP -

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Basic information

Entry
Database: PDB / ID: 1lor
Titlecrystal structure of orotidine 5'-monophosphate complexed with BMP
Componentsorotidine 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
6-HYDROXYURIDINE-5'-PHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 sequence Authors state that although residue 1 is MET and residue 101 is Arg according to the ... sequence Authors state that although residue 1 is MET and residue 101 is Arg according to the SwissProt entry, residue 1 was LEU and residue 101 was 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 monophosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2072
Polymers24,8671
Non-polymers3401
Water3,423190
1
A: orotidine monophosphate decarboxylase
hetero molecules

A: orotidine monophosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4144
Polymers49,7332
Non-polymers6802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area4800 Å2
ΔGint-40 kcal/mol
Surface area15200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.365, 103.796, 73.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological dimer can be generated by the two fold axis -x, y, -z+1/2

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Components

#1: Protein orotidine monophosphate decarboxylase / OMP decarboxylase / OMPDCASE


Mass: 24866.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Plasmid: pET15b / 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.: 1 / Source method: obtained synthetically / Formula: C9H13N2O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: trisodium citrate, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K
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
23-7 %dioxane1reservoir

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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: Feb 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 28942 / Num. obs: 28942 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.4 Å2
Reflection shellResolution: 1.6→1.63 Å / % possible all: 92.8
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 97 % / Num. measured all: 355820 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 92.8 % / Rmerge(I) obs: 0.085

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29.88 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 829656.88 / Data cutoff high rms absF: 829656.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2309 8 %RANDOM
Rwork0.173 ---
all0.173 28828 --
obs0.173 28828 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.7627 Å2 / ksol: 0.394807 e/Å3
Displacement parametersBiso mean: 15 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---2.86 Å20 Å2
3---3.56 Å2
Refine analyzeLuzzati coordinate error free: 0.17 Å / Luzzati sigma a free: 0.04 Å
Refinement stepCycle: LAST / Resolution: 1.6→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1582 0 22 190 1794
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.208 372 8.2 %
Rwork0.161 4170 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3BMP.PARAMBMP.TOP
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / Rfactor all: 0.173 / Rfactor Rfree: 0.196 / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.23
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.7 Å / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.161

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