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- PDB-1km0: Crystal structure of orotidine monophosphate decarboxylase mutant... -

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Basic information

Entry
Database: PDB / ID: 1km0
TitleCrystal structure of orotidine monophosphate decarboxylase mutant D70N complexed with 6-azaUMP
ComponentsOROTIDINE 5'-PHOSPHATE 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 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWu, N. / Gillon, W. / Pai, E.F.
CitationJournal: Biochemistry / Year: 2002
Title: Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography.
Authors: Wu, N. / Gillon, W. / Pai, E.F.
History
DepositionDec 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
B: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
C: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
D: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4808
Polymers107,1794
Non-polymers1,3014
Water8,773487
1
A: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
B: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2404
Polymers53,5902
Non-polymers6502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-40 kcal/mol
Surface area16200 Å2
MethodPISA
2
C: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
D: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2404
Polymers53,5902
Non-polymers6502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-41 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.761, 59.869, 73.878
Angle α, β, γ (deg.)97.27, 100.13, 106.93
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
Detailsbiological dimer

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Components

#1: Protein
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE / E.C.4.1.1.23 / OMP DECARBOXYLASE / OMPDCASE


Mass: 26794.863 Da / Num. of mol.: 4 / Mutation: D70N
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-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.: 487 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: trisodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
pH: 6.5 / Details: Wu, N., (2000) Acta Crystallogr., Sect.D, 56, 912.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
21.1 Mtrisodium citrate1reservoirpH6.5
33 %glycerol1reservoir

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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 / Details: bent conical Si-mirror (Rh coating)
RadiationMonochromator: bend cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 96504 / Num. obs: 96504 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.7 Å2
Reflection shellResolution: 1.7→1.81 Å / % possible all: 67.8
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Num. measured all: 452529 / Rmerge(I) obs: 0.038

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Processing

Software
NameVersionClassification
EPMRphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 603859.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS library
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3378 3.5 %RANDOM
Rwork0.179 ---
all0.179 96504 --
obs0.179 96504 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.5911 Å2 / ksol: 0.388701 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å2-0.11 Å20.35 Å2
2--0.72 Å2-2.68 Å2
3----2.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6822 0 84 487 7393
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.532
X-RAY DIFFRACTIONc_scangle_it3.72.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 412 3.5 %
Rwork0.23 11381 -
obs--67.8 %
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: 1.7 Å / Lowest resolution: 30 Å / Rfactor obs: 0.179 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.179
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_deg1.04
LS refinement shell
*PLUS
Rfactor Rfree: 0.258 / Rfactor Rwork: 0.23

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