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- PDB-1l2u: Orotidine 5'-monophosphate decarboxylase from E. coli -

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Basic information

Entry
Database: PDB / ID: 1l2u
TitleOrotidine 5'-monophosphate decarboxylase from E. coli
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / beta-alpha-barrel / homodimer / twinned crystals
Function / homology
Function and homology information


nucleobase-containing small molecule interconversion / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / carboxy-lyase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol / cytoplasm
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHarris, P. / Poulsen, J.C. / Jensen, K.F. / Larsen, S.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Substrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase
Authors: Harris, P. / Poulsen, J.C. / Jensen, K.F. / Larsen, S.
#1: Journal: Biochemistry / Year: 2000
Title: Structural basis for the catalytic mechanism of a proficient enzyme: Orotidine 5'-monophosphate decarboxylase
Authors: Harris, P. / Navarro Poulsen, J.C. / Jensen, K.F. / Larsen, S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase causes a change in crystal contacts and space group
Authors: Poulsen, J.C. / Harris, P. / Jensen, K.F. / Larsen, S.
History
DepositionFeb 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)52,7562
Polymers52,7562
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-20 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.690, 142.690, 105.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-1111-

HOH

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Components

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


Mass: 26378.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PLFF8 / Production host: Escherichia coli (E. coli)
References: UniProt: P08244, orotidine-5'-phosphate decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: sodium formate, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
22.5 Msodium formate1reservoir
30.1 Msodium acetate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 99.9 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0159 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 11, 2000 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0159 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. all: 42389 / Num. obs: 42389 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.091 / Net I/σ(I): 19
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2083 / % possible all: 99
Reflection
*PLUS
Num. obs: 42181 / % possible obs: 99.3 % / Rmerge(I) obs: 0.091

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1EIX

1eix


Resolution: 2.5→15 Å / Isotropic thermal model: isotropic / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.211 2032 in shells
Rwork0.159 --
all0.162 39834 -
obs0.162 35835 -
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 0 121 3512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.028
X-RAY DIFFRACTIONs_similar_dist0.06
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_zero_chiral_vol0.032
LS refinement shellResolution: 2.5→2.6 Å /
RfactorNum. reflection
Rwork0.254 -
obs-4379
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.4

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