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- PDB-3p5z: Crystal structure of the mutant T159S of orotidine 5'-monophospha... -

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Basic information

Entry
Database: PDB / ID: 3p5z
TitleCrystal structure of the mutant T159S 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 / N-PROPANOL / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesMethanobacterium thermoautotrophicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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)51,00211
Polymers49,7412
Non-polymers1,2619
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-40 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.666, 73.874, 59.523
Angle α, β, γ (deg.)90.00, 119.50, 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: 24870.672 Da / Num. of mol.: 2 / Mutation: T159S
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#5: 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% iso-propanol, 20% PEG 4000, 0.1M sodium citrate, 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: Aug 19, 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: 1.3→30.075 Å / Num. all: 104965 / Num. obs: 104965 / % possible obs: 96.84 % / 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: 1.3→30.075 Å / SU ML: 0.18 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1764 5244 5 %RANDOM
Rwork0.1647 ---
all0.1653 104965 --
obs0.1653 104965 96.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.805 Å2 / ksol: 0.374 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8579 Å20 Å20.0033 Å2
2--1.3373 Å2-0 Å2
3----0.4794 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 82 410 3828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063551
X-RAY DIFFRACTIONf_angle_d1.1134798
X-RAY DIFFRACTIONf_dihedral_angle_d15.6971389
X-RAY DIFFRACTIONf_chiral_restr0.073541
X-RAY DIFFRACTIONf_plane_restr0.007630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.31490.23951500.21622897X-RAY DIFFRACTION85
1.3149-1.33040.24421520.2143079X-RAY DIFFRACTION90
1.3304-1.34660.2091730.23140X-RAY DIFFRACTION92
1.3466-1.36370.21651650.19753246X-RAY DIFFRACTION94
1.3637-1.38160.20881520.1883299X-RAY DIFFRACTION95
1.3816-1.40050.22581700.18213260X-RAY DIFFRACTION96
1.4005-1.42050.18211750.18313285X-RAY DIFFRACTION96
1.4205-1.44170.20331800.17743255X-RAY DIFFRACTION96
1.4417-1.46430.19091620.16893331X-RAY DIFFRACTION97
1.4643-1.48830.1891690.16723311X-RAY DIFFRACTION97
1.4883-1.51390.17491620.16083306X-RAY DIFFRACTION97
1.5139-1.54150.19411800.16053326X-RAY DIFFRACTION97
1.5415-1.57110.18581700.16623393X-RAY DIFFRACTION97
1.5711-1.60320.19611720.1523315X-RAY DIFFRACTION97
1.6032-1.6380.18361550.15183372X-RAY DIFFRACTION98
1.638-1.67610.1611910.15233311X-RAY DIFFRACTION98
1.6761-1.7180.16111800.14693340X-RAY DIFFRACTION98
1.718-1.76450.17891650.14643398X-RAY DIFFRACTION98
1.7645-1.81640.15622190.14493345X-RAY DIFFRACTION99
1.8164-1.8750.16641730.13953371X-RAY DIFFRACTION99
1.875-1.9420.15461900.1393374X-RAY DIFFRACTION99
1.942-2.01980.15311690.143427X-RAY DIFFRACTION99
2.0198-2.11170.15262000.14073382X-RAY DIFFRACTION99
2.1117-2.2230.1381860.14543409X-RAY DIFFRACTION100
2.223-2.36220.16871660.15083449X-RAY DIFFRACTION99
2.3622-2.54450.16031690.1563418X-RAY DIFFRACTION99
2.5445-2.80040.17571990.15823402X-RAY DIFFRACTION99
2.8004-3.20520.15611960.16463339X-RAY DIFFRACTION98
3.2052-4.03670.14551690.14663488X-RAY DIFFRACTION100
4.0367-30.08340.18521850.17153453X-RAY DIFFRACTION98

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