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- PDB-1los: crystal structure of orotidine monophosphate decarboxylase mutant... -

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Basic information

Entry
Database: PDB / ID: 1los
Titlecrystal structure of orotidine monophosphate decarboxylase mutant deltaR203A complexed with 6-azaUMP
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-AZA URIDINE 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 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999 sequence Authors state that although residues 1, 1001, 2001 and 3001 are MET and residues 101, ... sequence Authors state that although residues 1, 1001, 2001 and 3001 are MET and residues 101, 1101, 2101 and 3101 are Arg according to the SwissProt entry, residues 1, 1001, 2001 and 3001 were LEU and residues 101, 1101, 2101 and 3101 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 monophosphate decarboxylase
B: orotidine monophosphate decarboxylase
C: orotidine monophosphate decarboxylase
D: orotidine monophosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1708
Polymers97,8694
Non-polymers1,3014
Water3,711206
1
A: orotidine monophosphate decarboxylase
B: orotidine monophosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5854
Polymers48,9342
Non-polymers6502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-43 kcal/mol
Surface area15780 Å2
MethodPISA
2
C: orotidine monophosphate decarboxylase
D: orotidine monophosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5854
Polymers48,9342
Non-polymers6502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-42 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.490, 56.152, 73.870
Angle α, β, γ (deg.)82.76, 89.89, 76.91
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a dimer.

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Components

#1: Protein
orotidine monophosphate decarboxylase / OMP decarboxylase / ompdcase / ompdecase


Mass: 24467.234 Da / Num. of mol.: 4 / Mutation: R203A
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-UP6 / 6-AZA URIDINE 5'-MONOPHOSPHATE / 6-AZA-UMP


Mass: 325.169 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H12N3O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: trisodium citrate, MgCl2, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mM1reservoirMgCl2
25 %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: Mar 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 58208 / Num. obs: 58208 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.3 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 64
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 489020 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 64 % / Rmerge(I) obs: 0.283

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Processing

Software
NameVersionClassification
EPMRphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.39 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1792 3.2 %RANDOM
Rwork0.205 ---
all0.205 56165 --
obs0.205 56165 87.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.3854 Å2 / ksol: 0.388375 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.9 Å2-2.21 Å2-0.63 Å2
2--7.11 Å24.09 Å2
3----1.21 Å2
Refine analyzeLuzzati coordinate error free: 0.28 Å / Luzzati sigma a free: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 84 206 6590
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_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_mcbond_it1.661.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it2.762
X-RAY DIFFRACTIONc_scangle_it3.992.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 181 2.8 %
Rwork0.305 6223 -
obs--59.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3AZA.PARAMAZA.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Rfactor all: 0.205 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.19
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Rfactor Rfree: 0.326 / Rfactor Rwork: 0.305

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