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- PDB-2bne: The structure of E. coli UMP kinase in complex with UMP -

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Basic information

Entry
Database: PDB / ID: 2bne
TitleThe structure of E. coli UMP kinase in complex with UMP
ComponentsURIDYLATE KINASE
KeywordsTRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE / PYRIMIDINE BIOSYNTHESIS
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleotide biosynthetic process / UDP biosynthetic process / phosphorylation / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Uridylate kinase, bacteria / Uridylate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / Uridylate kinase / Uridylate kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBriozzo, P. / Evrin, C. / Meyer, P. / Assairi, L. / Joly, N. / Barzu, O. / Gilles, A.M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure of Escherichia Coli Ump Kinase Differs from that of Other Nucleoside Monophosphate Kinases and Sheds New Light on Enzyme Regulation.
Authors: Briozzo, P. / Evrin, C. / Meyer, P. / Assairi, L. / Joly, N. / Barzu, O. / Gilles, A.M.
History
DepositionMar 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: URIDYLATE KINASE
B: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,29211
Polymers51,9992
Non-polymers1,2939
Water1,71195
1
A: URIDYLATE KINASE
B: URIDYLATE KINASE
hetero molecules

A: URIDYLATE KINASE
B: URIDYLATE KINASE
hetero molecules

A: URIDYLATE KINASE
B: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,87533
Polymers155,9966
Non-polymers3,87927
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)140.434, 140.434, 59.993
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein URIDYLATE KINASE / UMP KINASE / UK / URIDINE MONOPHOSPHATE KINASE


Mass: 25999.277 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P29464, UniProt: P0A7E9*PLUS, EC: 2.7.4.4
#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 158 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 158 TO ASN

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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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growpH: 8.5 / Details: pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 19016 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / % possible all: 93.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BND

2bnd


Resolution: 2.3→25 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 1847 9.4 %RANDOM
Rwork0.2065 ---
obs0.2065 18650 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.8104 Å2 / ksol: 0.361948 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.348 Å2-3.458 Å20 Å2
2---1.348 Å20 Å2
3---2.696 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 84 95 3739
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006107
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.18046
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GOL.PARAMGOL.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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