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- PDB-3nqe: Crystal structure of the mutant L123N of orotidine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 3nqe
TitleCrystal structure of the mutant L123N of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE/LYASE INHIBITOR / orotidine 5'-monophosphate decarboxylase / Methanobacterium thermoautotrophicum / inhibitor BMP / LYASE-LYASE INHIBITOR complex
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: 1.421 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2011
Title: Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site.
Authors: Iiams, V. / Desai, B.J. / Fedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Gerlt, J.A.
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Nov 2, 2011Group: Database references
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)50,6366
Polymers49,7712
Non-polymers8654
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-45 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.915, 63.982, 61.753
Angle α, β, γ (deg.)90.00, 115.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24885.643 Da / Num. of mol.: 2 / Mutation: L123N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: pyrF, MTH_129 / 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.: 2 / Source method: obtained synthetically / Formula: C9H13N2O10P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 42.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG2000, 0.1M potassium thiocyanate , 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: Apr 22, 2010
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: 1.421→32.426 Å / Num. all: 78628 / Num. obs: 78628 / % possible obs: 99.34 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.079

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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: PDB entry 3G18

3g18


Resolution: 1.421→32.426 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 3956 5.03 %RANDOM
Rwork0.1801 ---
all0.1814 78628 --
obs0.1814 78628 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.963 Å2 / ksol: 0.391 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2081 Å20 Å2-0.6059 Å2
2--2.1571 Å20 Å2
3---0.0509 Å2
Refinement stepCycle: LAST / Resolution: 1.421→32.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 56 432 3803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063502
X-RAY DIFFRACTIONf_angle_d1.1024746
X-RAY DIFFRACTIONf_dihedral_angle_d15.8711360
X-RAY DIFFRACTIONf_chiral_restr0.073537
X-RAY DIFFRACTIONf_plane_restr0.006628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4215-1.43880.19851030.1972378X-RAY DIFFRACTION89
1.4388-1.4570.22291680.19022611X-RAY DIFFRACTION99
1.457-1.47620.21141590.18752654X-RAY DIFFRACTION100
1.4762-1.49640.20031460.17822639X-RAY DIFFRACTION99
1.4964-1.51780.19731260.17592670X-RAY DIFFRACTION100
1.5178-1.54040.20691400.17952682X-RAY DIFFRACTION99
1.5404-1.56450.21151340.17782642X-RAY DIFFRACTION99
1.5645-1.59020.21051430.18042665X-RAY DIFFRACTION100
1.5902-1.61760.20771550.17572665X-RAY DIFFRACTION100
1.6176-1.6470.20921270.17772656X-RAY DIFFRACTION100
1.647-1.67870.21361310.1832692X-RAY DIFFRACTION100
1.6787-1.71290.22441360.1752700X-RAY DIFFRACTION100
1.7129-1.75020.18381400.17712668X-RAY DIFFRACTION100
1.7502-1.79090.19321510.16672633X-RAY DIFFRACTION100
1.7909-1.83570.18451570.16472664X-RAY DIFFRACTION100
1.8357-1.88530.19851340.16542699X-RAY DIFFRACTION100
1.8853-1.94080.18171380.16532705X-RAY DIFFRACTION100
1.9408-2.00340.18411180.16582676X-RAY DIFFRACTION100
2.0034-2.0750.20681420.16992708X-RAY DIFFRACTION100
2.075-2.15810.20651460.17382657X-RAY DIFFRACTION100
2.1581-2.25630.18121420.17132682X-RAY DIFFRACTION100
2.2563-2.37520.21511290.17462724X-RAY DIFFRACTION100
2.3752-2.52390.19151410.18692688X-RAY DIFFRACTION100
2.5239-2.71870.2321650.18442675X-RAY DIFFRACTION100
2.7187-2.99210.21271220.19852691X-RAY DIFFRACTION100
2.9921-3.42470.21351500.18472719X-RAY DIFFRACTION100
3.4247-4.31320.17621580.15342707X-RAY DIFFRACTION100
4.3132-32.43450.19531550.1742722X-RAY DIFFRACTION99

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