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- PDB-4dbe: Crystal structure of orotidine 5'-monophosphate decarboxylase fro... -

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Basic information

Entry
Database: PDB / ID: 4dbe
TitleCrystal structure of orotidine 5'-monophosphate decarboxylase from Sulfolobus solfataricus complexed with inhibitor BMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE/LYASE INHIBITOR / TIM barrel / orotidine 5'-monophosphate decarboxylase / 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
Similarity search - Function
: / Orotidine 5'-phosphate decarboxylase / 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 speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.789 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of orotidine 5'-monophosphate decarboxylase from Sulfolobus solfataricus complexed with inhibitor BMP
Authors: Fedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C.
History
DepositionJan 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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'-phosphate decarboxylase
B: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5218
Polymers49,4682
Non-polymers1,0536
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-48 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.414, 41.536, 73.117
Angle α, β, γ (deg.)90.00, 94.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24733.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: 98/2 / Gene: pyrF, Ssol_1680 / Production host: Escherichia coli (E. coli)
References: UniProt: D0KT28, 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG ME 550, 0.1M MES, 0.01M Zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.789→32.751 Å / Num. all: 41028 / Num. obs: 41028 / % possible obs: 99.15 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DBD

4dbd


Resolution: 1.789→32.751 Å / SU ML: 0.48 / σ(F): 0 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 2062 5.03 %RANDOM
Rwork0.1953 ---
all0.1973 41028 --
obs0.1973 41028 99.15 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.878 Å2 / ksol: 0.396 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.31 Å2-0 Å2-3.8325 Å2
2---2.7631 Å2-0 Å2
3----6.5469 Å2
Refinement stepCycle: LAST / Resolution: 1.789→32.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 67 129 3515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073459
X-RAY DIFFRACTIONf_angle_d1.0224662
X-RAY DIFFRACTIONf_dihedral_angle_d13.4941349
X-RAY DIFFRACTIONf_chiral_restr0.07536
X-RAY DIFFRACTIONf_plane_restr0.004576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7893-1.8310.3751120.36422281X-RAY DIFFRACTION88
1.831-1.87670.30431680.30212576X-RAY DIFFRACTION100
1.8767-1.92750.3311370.2792569X-RAY DIFFRACTION100
1.9275-1.98420.28521380.24462614X-RAY DIFFRACTION100
1.9842-2.04820.26721450.2262603X-RAY DIFFRACTION100
2.0482-2.12140.26461540.22152572X-RAY DIFFRACTION100
2.1214-2.20630.25041300.20692626X-RAY DIFFRACTION100
2.2063-2.30670.2431280.19612613X-RAY DIFFRACTION100
2.3067-2.42830.26261330.19042601X-RAY DIFFRACTION100
2.4283-2.58040.26911390.20142629X-RAY DIFFRACTION100
2.5804-2.77950.22421390.20112630X-RAY DIFFRACTION100
2.7795-3.05910.30251360.19892606X-RAY DIFFRACTION100
3.0591-3.50130.24431370.19622643X-RAY DIFFRACTION100
3.5013-4.40950.19841260.15742669X-RAY DIFFRACTION100
4.4095-32.75640.16631400.16772734X-RAY DIFFRACTION100

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