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- PDB-2f3r: Crystal Structure Of E.coli Guanylate Kinase In Complex With Ap5G -

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Basic information

Entry
Database: PDB / ID: 2f3r
TitleCrystal Structure Of E.coli Guanylate Kinase In Complex With Ap5G
ComponentsGuanylate kinase
KeywordsTRANSFERASE / GMP KINASE / GUANYLATE KINASE / NUCLEOTIDE ANALOGUE
Function / homology
Function and homology information


guanylate kinase / guanylate kinase activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
Guanylate kinase / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. ...Guanylate kinase / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE / Guanylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsHible, G. / Cherfils, J.
CitationJournal: Biochimie / Year: 2006
Title: Crystal structures of GMP kinase in complex with ganciclovir monophosphate and Ap5G.
Authors: Hible, G. / Daalova, P. / Gilles, A.M. / Cherfils, J.
History
DepositionNov 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanylate kinase
B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1164
Polymers47,2512
Non-polymers1,8652
Water46826
1
A: Guanylate kinase
B: Guanylate kinase
hetero molecules

A: Guanylate kinase
B: Guanylate kinase
hetero molecules

A: Guanylate kinase
B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,34912
Polymers141,7546
Non-polymers5,5946
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area23240 Å2
ΔGint-82 kcal/mol
Surface area53060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.527, 67.527, 149.703
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF A DIMER (CHAINS A and B). The biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -y, x-y, z and -x+y, -x, z.

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Components

#1: Protein Guanylate kinase / GMP kinase


Mass: 23625.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gmk, spoR / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BLI5 / References: UniProt: P60546, guanylate kinase
#2: Chemical ChemComp-G5P / P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE


Mass: 932.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O23P5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 4000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→28 Å / Num. all: 13344 / Num. obs: 13344 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.2
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 7 / Num. unique all: 2192 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2AN9

2an9


Resolution: 2.5→27.96 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1728695.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 674 5.1 %RANDOM
Rwork0.211 ---
all0.211 13344 --
obs0.211 13344 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.4334 Å2 / ksol: 0.312595 e/Å3
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.21 Å211.77 Å20 Å2
2--2.86 Å20 Å2
3----7.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→27.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 116 26 3355
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it2.241.5
X-RAY DIFFRACTIONc_mcangle_it3.82
X-RAY DIFFRACTIONc_scbond_it3.312
X-RAY DIFFRACTIONc_scangle_it5.332.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 86 3.9 %
Rwork0.252 2106 -
obs-2192 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramG5P.CNS.top
X-RAY DIFFRACTION3G5P.CNS.paramwater.top

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