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

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Basic information

Entry
Database: PDB / ID: 4lui
TitleCrystal structure of Orotidine 5'-monophosphate decarboxylase from methanocaldococcus jannaschii
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / tim barrel fold / 5'-MONOPHOSPHATE DECARBOXYLASE
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
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
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

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)51,6343
Polymers51,5982
Non-polymers351
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-40 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.880, 49.783, 168.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG ME 2000, 0.1M Tris, 0.2M trimethylamine N-oxide, pH 8.5, 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→42.151 Å / Num. all: 54179 / Num. obs: 54179 / % possible obs: 99.57 % / 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→42.151 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 21.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1686 3.11 %RANDOM
Rwork0.1747 ---
obs0.1755 54179 99.57 %-
all-54179 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→42.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 1 377 3629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063340
X-RAY DIFFRACTIONf_angle_d1.0434510
X-RAY DIFFRACTIONf_dihedral_angle_d11.6841314
X-RAY DIFFRACTIONf_chiral_restr0.071541
X-RAY DIFFRACTIONf_plane_restr0.006570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64480.26171300.25864096X-RAY DIFFRACTION95
1.6448-1.69790.28441470.23644286X-RAY DIFFRACTION100
1.6979-1.75860.271500.21974335X-RAY DIFFRACTION100
1.7586-1.8290.27031380.20144350X-RAY DIFFRACTION100
1.829-1.91230.21981340.18954363X-RAY DIFFRACTION100
1.9123-2.01310.21171230.18774347X-RAY DIFFRACTION100
2.0131-2.13920.22461280.17474360X-RAY DIFFRACTION100
2.1392-2.30440.20671170.17614440X-RAY DIFFRACTION100
2.3044-2.53630.22541460.18244368X-RAY DIFFRACTION100
2.5363-2.90320.19081480.18584427X-RAY DIFFRACTION100
2.9032-3.65740.20051560.16634472X-RAY DIFFRACTION100
3.6574-42.16570.15831690.14834649X-RAY DIFFRACTION100
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)
11.13390.00830.17551.3069-0.00132.0220.02050.0955-0.0673-0.22650.05180.28410.0905-0.1941-0.04480.1333-0.0046-0.04010.1383-0.00730.179480.376245.914912.7339
21.04290.09060.24091.66530.12231.1921-0.0064-0.01150.0320.0250.033-0.1211-0.04930.1161-0.02410.09390.01240.02450.1293-0.01130.1102.174355.274927.96
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA18 - 230
2X-RAY DIFFRACTION2CHAIN BB19 - 232

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