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- PDB-1eix: STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COL... -

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Basic information

Entry
Database: PDB / ID: 1eix
TitleSTRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP
ComponentsOROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
KeywordsLYASE / alpha-beta-barrel / protein-inhibitor complex / homodimer
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 / cytoplasm / 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
Chem-BMQ / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsHarris, P. / Poulsen, J.C.N. / Jensen, K.F. / Larsen, S.
CitationJournal: Biochemistry / Year: 2000
Title: Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase.
Authors: Harris, P. / Poulsen, J.C.N. / Jensen, K.F. / Larsen, S.
History
DepositionFeb 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
B: OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
C: OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
D: OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8748
Polymers105,5134
Non-polymers1,3614
Water6,828379
1
A: OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
B: OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4374
Polymers52,7562
Non-polymers6802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-26 kcal/mol
Surface area16890 Å2
MethodPISA
2
C: OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
D: OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4374
Polymers52,7562
Non-polymers6802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-24 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.280, 95.920, 145.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer constructed from chain A and B (or C and D) which are connected by a twofold.

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Components

#1: Protein
OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE


Mass: 26378.225 Da / Num. of mol.: 4
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: Chemical
ChemComp-BMQ / 1-(5'-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC ACID


Type: RNA linking / Mass: 340.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O10P / Details: SIGMA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
128 %PEG80001reservoir
20.2 M1reservoirMgCl2
30.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9902
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9902 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 102335 / Num. obs: 29678 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.243 / Num. unique all: 4946 / % possible all: 98
Reflection
*PLUS
Num. measured all: 102335
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 92.4 % / Mean I/σ(I) obs: 5.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementResolution: 2.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1461 -random
Rwork0.191 ---
all0.194 29678 --
obs0.194 29640 98 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7007 0 88 379 7474
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.007
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3

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