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

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Basic information

Entry
Database: PDB / ID: 4muz
TitleCrystal structure of orotidine 5'-monophosphate decarboxylase from Archaeoglobus fulgidus 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 speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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 Archaeoglobus fulgidus complexed with inhibitor BMP
Authors: Fedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C.
History
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references / Structure summary
Revision 1.2Sep 20, 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'-phosphate decarboxylase
B: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3506
Polymers49,4862
Non-polymers8654
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-47 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.933, 58.480, 56.914
Angle α, β, γ (deg.)90.00, 94.98, 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: 24742.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: pyrF, AF_0929 / Production host: Escherichia coli (E. coli)
References: UniProt: O29333, 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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 411 / 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: 1.84 Å3/Da / Density % sol: 33.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 20% PEG 8000, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.39→40.708 Å / Num. all: 71632 / Num. obs: 71632 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LTP

3ltp


Resolution: 1.39→40.708 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 2165 3.02 %RANDOM
Rwork0.1617 ---
obs0.1624 71632 99 %-
all-71632 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→40.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 56 411 3665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073458
X-RAY DIFFRACTIONf_angle_d1.1094684
X-RAY DIFFRACTIONf_dihedral_angle_d12.4751372
X-RAY DIFFRACTIONf_chiral_restr0.075539
X-RAY DIFFRACTIONf_plane_restr0.006602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3897-1.4220.28281420.23824425X-RAY DIFFRACTION95
1.422-1.45750.21271620.21264620X-RAY DIFFRACTION99
1.4575-1.4970.24981420.2024591X-RAY DIFFRACTION99
1.497-1.5410.23441350.18424680X-RAY DIFFRACTION99
1.541-1.59070.24251240.17864617X-RAY DIFFRACTION100
1.5907-1.64760.19641430.174625X-RAY DIFFRACTION99
1.6476-1.71360.20551360.1654653X-RAY DIFFRACTION99
1.7136-1.79160.19551580.16894600X-RAY DIFFRACTION99
1.7916-1.8860.17651500.15754640X-RAY DIFFRACTION99
1.886-2.00420.19761470.15734616X-RAY DIFFRACTION99
2.0042-2.15890.16921300.15824663X-RAY DIFFRACTION99
2.1589-2.37610.16111420.15564657X-RAY DIFFRACTION100
2.3761-2.71990.19771420.15854697X-RAY DIFFRACTION100
2.7199-3.42650.17081480.16174698X-RAY DIFFRACTION100
3.4265-40.7250.17081640.14464685X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0590.11940.23570.89010.15550.77370.0303-0.0607-0.05040.08480.0059-0.06620.03270.0347-0.03410.07840.0099-0.00220.07060.00440.073745.084318.250152.4924
20.90980.15610.30490.73980.16391.0063-0.02960.02560.0292-0.09580.01250.0665-0.0331-0.03140.01630.08760.0025-0.00650.06550.00760.089528.87328.078433.8325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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