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- PDB-4luj: Crystal structure of Orotidine 5'-monophosphate decarboxylase fro... -

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Basic information

Entry
Database: PDB / ID: 4luj
TitleCrystal structure of Orotidine 5'-monophosphate decarboxylase from methanocaldococcus jannaschii complexed with inhibitor BMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLyase/Lyase inhibitor / tim barrel fold / 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 / 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 speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 methanocaldococcus jannaschii complexed with inhibitor BMP
Authors: Fedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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

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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)52,2794
Polymers51,5982
Non-polymers6802
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-37 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.811, 47.567, 85.714
Angle α, β, γ (deg.)90.00, 90.02, 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: 25799.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: pyrF, MJ0252 / Production host: Escherichia coli (E. coli)
References: UniProt: Q57700, 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 / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 1.89 Å3/Da / Density % sol: 34.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium chloride, 0.1M hepes, 20% PEG 3000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Jul 20, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.6→33.721 Å / Num. all: 51183 / Num. obs: 51183 / % possible obs: 99.64 % / 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: PDB entry 3LTP

3ltp


Resolution: 1.6→33.721 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 1596 3.12 %RANDOM
Rwork0.179 ---
obs0.1797 51183 99.64 %-
all-51183 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→33.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 44 174 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063488
X-RAY DIFFRACTIONf_angle_d1.0284719
X-RAY DIFFRACTIONf_dihedral_angle_d13.2931419
X-RAY DIFFRACTIONf_chiral_restr0.07559
X-RAY DIFFRACTIONf_plane_restr0.006595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64870.32681440.3044371X-RAY DIFFRACTION97
1.6487-1.70760.28731600.26024444X-RAY DIFFRACTION100
1.7076-1.7760.27471430.22984514X-RAY DIFFRACTION100
1.776-1.85680.24791410.19974450X-RAY DIFFRACTION100
1.8568-1.95470.23831360.18884527X-RAY DIFFRACTION100
1.9547-2.07720.20621310.17464539X-RAY DIFFRACTION100
2.0772-2.23750.2031360.17244491X-RAY DIFFRACTION100
2.2375-2.46260.19391680.18214500X-RAY DIFFRACTION100
2.4626-2.81880.24641570.19434537X-RAY DIFFRACTION100
2.8188-3.55080.18511460.18744552X-RAY DIFFRACTION100
3.5508-33.72840.15181340.14564662X-RAY DIFFRACTION100
Refinement TLS params.

S32: 0.1773 Å ° / 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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3069-0.02-0.00032.3555-1.1113.311-0.0478-0.1567-0.19240.1275-0.0795-0.10520.20350.11140.27640.0140.02150.17830.03190.2505-37.2764-21.759631.0866
21.36690.1-0.05692.4309-1.03333.2263-0.03810.15640.1944-0.1245-0.0784-0.1097-0.19350.10640.2757-0.0122-0.02450.17540.03720.2421-37.2831-1.937911.9902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA20 - 233
2X-RAY DIFFRACTION2CHAIN BB20 - 233

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