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- PDB-1jjk: Selenomethionine Substitution of Orotidine-5'-monophosphate Decar... -

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Basic information

Entry
Database: PDB / ID: 1jjk
TitleSelenomethionine Substitution of Orotidine-5'-monophosphate Decarboxylase from E. coli Causes a Change in Crystal Contacts and Space Group
ComponentsOROTIDINE 5'-PHOSPHATE 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
6-HYDROXYURIDINE-5'-PHOSPHATE / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsPoulsen, J.-C.N. / Harris, P. / Jensen, K.F. / Larsen, S.
Citation
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.
#1: Journal: 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
DepositionJul 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
C: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
D: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
E: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
F: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
G: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
H: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
I: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
J: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
K: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
L: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
M: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
N: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
O: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
P: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,24732
Polymers428,80416
Non-polymers5,44316
Water00
1
A: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
B: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2814
Polymers53,6012
Non-polymers6802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-24 kcal/mol
Surface area16990 Å2
MethodPISA
2
C: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
D: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2814
Polymers53,6012
Non-polymers6802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-23 kcal/mol
Surface area16980 Å2
MethodPISA
3
E: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
F: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2814
Polymers53,6012
Non-polymers6802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-26 kcal/mol
Surface area17000 Å2
MethodPISA
4
G: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
H: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2814
Polymers53,6012
Non-polymers6802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-26 kcal/mol
Surface area16990 Å2
MethodPISA
5
I: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
J: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2814
Polymers53,6012
Non-polymers6802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-25 kcal/mol
Surface area17000 Å2
MethodPISA
6
K: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
L: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2814
Polymers53,6012
Non-polymers6802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-25 kcal/mol
Surface area17010 Å2
MethodPISA
7
M: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
N: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2814
Polymers53,6012
Non-polymers6802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-26 kcal/mol
Surface area16950 Å2
MethodPISA
8
O: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
P: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2814
Polymers53,6012
Non-polymers6802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-23 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.5, 149.0, 115.6
Angle α, β, γ (deg.)90, 115.3, 90
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer constructed like AB, CD, EF, GH, IJ, KL, MN or OP

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Components

#1: Protein
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE / OMP DECARBOXYLASE


Mass: 26800.279 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pLFF8 / Production host: Escherichia coli (E. coli) / Strain (production host): SO6735
References: UniProt: P08244, orotidine-5'-phosphate decarboxylase
#2: Chemical
ChemComp-BMP / 6-HYDROXYURIDINE-5'-PHOSPHATE


Type: RNA linking / Mass: 340.181 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C9H13N2O10P
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 291 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.0 mg/mlprotein1drop
220 %PEG80001reservoir
30.2 M1reservoirMgCl2
40.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9787, 0.9789, 0.8856
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 9, 1999
RadiationMonochromator: Si(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.97891
30.88561
ReflectionResolution: 3→30 Å / Num. all: 64921 / Num. obs: 64921 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 3.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 1.3 / Num. unique all: 9615 / % possible all: 93.7
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 333946

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
MAR345data collection
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & huber
RfactorNum. reflection% reflectionSelection details
Rfree0.344 3281 -random
Rwork0.3441 ---
all0.3435 64880 --
obs0.3435 64880 91.5 %-
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27984 0 352 0 28336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 3→3.02 Å
RfactorNum. reflection
Rfree0.387 70
Rwork0.423 -
obs-1315
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3
LS refinement shell
*PLUS
Highest resolution: 3 Å / Rfactor Rfree: 0.387 / Rfactor Rwork: 0.423

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