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- PDB-3p61: Crystal structure of the mutant R160A of orotidine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 3p61
TitleCrystal structure of the mutant R160A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP
ComponentsOrotidine 5'-monophosphate decarboxylase
KeywordsLYASE / tim barrel / orotidine 5'-monophosphate decarboxylase / inhibitor BMP
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 speciesMethanobacterium thermoautotrophicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.396 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2012
Title: Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.
Authors: Desai, B.J. / Wood, B.M. / Fedorov, A.A. / Fedorov, E.V. / Goryanova, B. / Amyes, T.L. / Richard, J.P. / Almo, S.C. / Gerlt, J.A.
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 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

Downloads & links

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Assembly

Deposited unit
A: Orotidine 5'-monophosphate decarboxylase
B: Orotidine 5'-monophosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2784
Polymers49,5972
Non-polymers6802
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-44 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.803, 64.431, 61.779
Angle α, β, γ (deg.)90.00, 115.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24798.582 Da / Num. of mol.: 2 / Mutation: R160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobacterium thermoautotrophicum (archaea)
Strain: Delta H / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4000, 0.1M sodium citrate, 0.2M ammomium acetate, pH 5.6, 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: Jul 16, 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: 1.396→21.264 Å / Num. all: 76701 / Num. obs: 76701 / % possible obs: 91.47 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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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: 3LTP

3ltp


Resolution: 1.396→21.264 Å / SU ML: 0.17 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 3851 5.02 %RANDOM
Rwork0.1988 ---
all0.1999 76701 --
obs0.1999 76701 91.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.838 Å2 / ksol: 0.403 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9653 Å2-0 Å2-3.4405 Å2
2--0.7114 Å2-0 Å2
3---0.2539 Å2
Refinement stepCycle: LAST / Resolution: 1.396→21.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 44 410 3749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063453
X-RAY DIFFRACTIONf_angle_d1.14681
X-RAY DIFFRACTIONf_dihedral_angle_d15.3651336
X-RAY DIFFRACTIONf_chiral_restr0.075531
X-RAY DIFFRACTIONf_plane_restr0.006620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3963-1.41340.3188570.27561328X-RAY DIFFRACTION46
1.4134-1.43120.3129950.25981605X-RAY DIFFRACTION57
1.4312-1.45010.28751050.24181718X-RAY DIFFRACTION62
1.4501-1.46990.2631980.23891954X-RAY DIFFRACTION69
1.4699-1.49090.21921000.22782081X-RAY DIFFRACTION73
1.4909-1.51320.26641140.23082277X-RAY DIFFRACTION80
1.5132-1.53680.26211200.23612451X-RAY DIFFRACTION85
1.5368-1.5620.23611190.22642572X-RAY DIFFRACTION92
1.562-1.58890.22051250.21282804X-RAY DIFFRACTION98
1.5889-1.61780.24971610.20312851X-RAY DIFFRACTION100
1.6178-1.64890.25021480.20082796X-RAY DIFFRACTION100
1.6489-1.68260.20261530.21722857X-RAY DIFFRACTION100
1.6826-1.71910.2511480.21522858X-RAY DIFFRACTION100
1.7191-1.75910.21771470.20752817X-RAY DIFFRACTION100
1.7591-1.80310.23491710.20872813X-RAY DIFFRACTION100
1.8031-1.85180.2041610.19782802X-RAY DIFFRACTION100
1.8518-1.90630.24851600.19642850X-RAY DIFFRACTION100
1.9063-1.96770.20961440.18282811X-RAY DIFFRACTION100
1.9677-2.0380.21091490.17992848X-RAY DIFFRACTION100
2.038-2.11950.18951350.18082876X-RAY DIFFRACTION100
2.1195-2.21590.21541330.18492860X-RAY DIFFRACTION100
2.2159-2.33260.22441700.19092818X-RAY DIFFRACTION100
2.3326-2.47850.21221530.1992875X-RAY DIFFRACTION100
2.4785-2.66960.21141350.19812847X-RAY DIFFRACTION100
2.6696-2.93760.25021610.20972855X-RAY DIFFRACTION100
2.9376-3.36120.22541670.20242836X-RAY DIFFRACTION100
3.3612-4.22930.18741600.17272870X-RAY DIFFRACTION100
4.2293-21.26620.18851620.17672920X-RAY DIFFRACTION100

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