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- PDB-3m47: Crystal structure of the mutant I218A of orotidine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 3m47
TitleCrystal structure of the mutant I218A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / orotidine 5'-monophosphate decarboxylase / mutant I218A
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
Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2010
Title: Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.
Authors: Wood, B.M. / Amyes, T.L. / Fedorov, A.A. / Fedorov, E.V. / Shabila, A. / Almo, S.C. / Richard, J.P. / Gerlt, J.A.
History
DepositionMar 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2388
Polymers49,6852
Non-polymers5536
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-31 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.905, 56.908, 125.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24842.617 Da / Num. of mol.: 2 / Mutation: I218A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli)
References: UniProt: O26232, orotidine-5'-phosphate decarboxylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.2→33.7 Å / Num. all: 98323 / Num. obs: 98323 / % possible obs: 77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.083

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G18

3g18


Resolution: 1.2→33.7 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 4909 4.99 %RANDOM
Rwork0.2265 ---
all0.2276 98323 --
obs0.2276 98323 76.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.589 Å2 / ksol: 0.424 e/Å3
Refinement stepCycle: LAST / Resolution: 1.2→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 36 238 3481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063330
X-RAY DIFFRACTIONf_angle_d1.0844490
X-RAY DIFFRACTIONf_dihedral_angle_d14.4831254
X-RAY DIFFRACTIONf_chiral_restr0.075511
X-RAY DIFFRACTIONf_plane_restr0.006591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21380.198230.4923114X-RAY DIFFRACTION3
1.2138-1.22810.631240.4284104X-RAY DIFFRACTION3
1.2281-1.24310.49330.471351X-RAY DIFFRACTION1
1.2431-1.25880.4135140.4094145X-RAY DIFFRACTION4
1.2588-1.27540.453980.4556186X-RAY DIFFRACTION5
1.2754-1.29280.3849230.4445695X-RAY DIFFRACTION17
1.2928-1.31130.388650.4021254X-RAY DIFFRACTION32
1.3113-1.33090.41380.38242605X-RAY DIFFRACTION65
1.3309-1.35170.31811790.39083339X-RAY DIFFRACTION82
1.3517-1.37380.38681950.37443682X-RAY DIFFRACTION93
1.3738-1.39750.36911920.3553990X-RAY DIFFRACTION99
1.3975-1.42290.32912000.3394015X-RAY DIFFRACTION100
1.4229-1.45030.31421910.32094018X-RAY DIFFRACTION100
1.4503-1.47990.30772140.30114009X-RAY DIFFRACTION100
1.4799-1.51210.29431970.29554067X-RAY DIFFRACTION100
1.5121-1.54730.27972030.27434024X-RAY DIFFRACTION100
1.5473-1.5860.30752090.2584019X-RAY DIFFRACTION100
1.586-1.62880.27282040.24714059X-RAY DIFFRACTION100
1.6288-1.67680.26362280.24634014X-RAY DIFFRACTION100
1.6768-1.73090.26312060.2414022X-RAY DIFFRACTION100
1.7309-1.79270.27712220.23754034X-RAY DIFFRACTION100
1.7927-1.86450.26872250.22954035X-RAY DIFFRACTION100
1.8645-1.94940.24262090.22074040X-RAY DIFFRACTION100
1.9494-2.05210.22142160.2074085X-RAY DIFFRACTION100
2.0521-2.18070.23112250.22014066X-RAY DIFFRACTION100
2.1807-2.3490.25242060.22024061X-RAY DIFFRACTION100
2.349-2.58530.25472250.22934123X-RAY DIFFRACTION100
2.5853-2.95920.24222460.22044092X-RAY DIFFRACTION100
2.9592-3.72760.22912160.20554168X-RAY DIFFRACTION100
3.7276-33.7110.21582430.19524298X-RAY DIFFRACTION99

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