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

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Basic information

Entry
Database: PDB / ID: 2bnf
TitleThe structure of E. coli UMP kinase in complex with UTP
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'-TRIPHOSPHATE / Uridylate kinase / Uridylate kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 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 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)54,73711
Polymers53,1242
Non-polymers1,6139
Water1,33374
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)164,21133
Polymers159,3726
Non-polymers4,83927
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)141.910, 141.910, 60.380
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: 26562.018 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P29464, UniProt: P0A7E9*PLUS, EC: 2.7.4.4
#2: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#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.: 74 / 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: 2.23 Å3/Da / Density % sol: 44.45 %
Crystal growpH: 8.5 / Details: pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.981019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981019 Å / Relative weight: 1
ReflectionResolution: 2.45→35 Å / Num. obs: 33118 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9
Reflection shellHighest resolution: 2.45 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→35 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 745 4.5 %RANDOM
Rwork0.1836 ---
obs0.1836 15479 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.9327 Å2 / ksol: 0.36074 e/Å3
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.786 Å2-5.535 Å20 Å2
2---2.786 Å20 Å2
3---5.571 Å2
Refinement stepCycle: LAST / Resolution: 2.45→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3571 0 100 74 3745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006695
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_deg1.23014
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 DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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