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- PDB-2anb: Crystal Structure Of Oligomeric E.coli Guanylate Kinase In Comple... -

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Basic information

Entry
Database: PDB / ID: 2anb
TitleCrystal Structure Of Oligomeric E.coli Guanylate Kinase In Complex With GMP
ComponentsGuanylate kinase
KeywordsTRANSFERASE / GMP kinase / guanylate kinase / oligomeric
Function / homology
Function and homology information


guanylate kinase / GMP kinase activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase / 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 phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase / 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
GUANOSINE-5'-MONOPHOSPHATE / Guanylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHible, G. / Renault, L. / Schaeffer, F. / Christova, P. / Radulescu, A.Z. / Evrin, C. / Gilles, A.M. / Cherfils, J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase
Authors: Hible, G. / Renault, L. / Schaeffer, F. / Christova, P. / Radulescu, A.Z. / Evrin, C. / Gilles, A.M. / Cherfils, J.
History
DepositionAug 11, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 25, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0853
Polymers23,6261
Non-polymers4592
Water21612
1
A: Guanylate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)144,51018
Polymers141,7546
Non-polymers2,75612
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
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
MethodPQS
2
A: Guanylate kinase
hetero molecules

A: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1706
Polymers47,2512
Non-polymers9194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area5140 Å2
ΔGint-77 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.728, 106.728, 155.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF A MONOMER. The biological assembly is a hexamer generated from the monomer in the asymmetric unit by the 5 operations: 1:matrix= ( -0.50000 -0.86603 0.00000 ) ( 0.86603 -0.50000 0.00000 ) ( 0.00000 0.00000 1.00000 ) translation= ( 106.72798 -0.00010 0.00001 ) 2: matrix= ( -0.50000 0.86603 0.00000 ) ( -0.86603 -0.50000 0.00000 ) ( 0.00000 0.00000 1.00000 ) translation= ( 53.36393 92.42904 -0.00008 ) 3:matrix= ( -0.50000 0.86602 0.00000 ) ( 0.86602 0.50000 0.00000 ) ( 0.00000 0.00000 -1.00000 ) translation= ( 53.36408 -30.80985 103.51692 ) 4:matrix= ( -0.50000 -0.86603 0.00000 ) ( -0.86603 0.50000 0.00000 ) ( 0.00000 0.00000 -1.00000 ) translation= ( 106.72797 61.61937 103.51704 ) 5:matrix= ( 1.00000 0.00000 0.00000 ) ( 0.00000 -1.00000 0.00000 ) ( 0.00000 0.00000 -1.00000 ) translation= ( 0.00000 61.61900 103.51700 )

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Components

#1: Protein Guanylate kinase / GMP kinase


Mass: 23625.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gmk / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BLI5 / References: UniProt: P60546, guanylate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.62 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.4M ammonium sulfate, 0.2M lithium chloride, 0.1M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.9→19 Å / Num. all: 7689 / Num. obs: 7689 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 67.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.6
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 5.8 / Num. unique all: 553 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AN9

2an9


Resolution: 2.9→19 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.365 / SU ML: 0.28 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.004 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24181 368 4.8 %RANDOM
Rwork0.20338 ---
all0.20509 7354 --
obs0.20509 7354 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.637 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 29 12 1691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211709
X-RAY DIFFRACTIONr_bond_other_d0.0020.021531
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9632314
X-RAY DIFFRACTIONr_angle_other_deg0.79233550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021889
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02355
X-RAY DIFFRACTIONr_nbd_refined0.2140.2360
X-RAY DIFFRACTIONr_nbd_other0.2150.21756
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21096
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3541.51025
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71721649
X-RAY DIFFRACTIONr_scbond_it1.1323684
X-RAY DIFFRACTIONr_scangle_it2.0664.5665
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 27 -
Rwork0.245 526 -
obs-553 99.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7248-0.3222-0.53913.681-1.22382.2221-0.40630.1270.12080.2739-0.0260.0753-0.2068-0.24250.43230.0438-0.03860.01980.3361-0.1920.153634.30730.60662.019
29.58-2.3266-3.346411.53421.19167.1559-1.177-1.6744-0.94261.33040.7602-0.4990.70630.3360.41680.36430.27070.21940.54060.09040.219331.55922.66381.839
312.2742-1.11.73031.5025-0.48468.465-0.8985-0.7161-2.2680.84130.07840.30791.2405-0.0940.82010.4806-0.04180.56990.2212-0.03541.031240.0618.00970.188
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 352 - 35
2X-RAY DIFFRACTION1AA87 - 12787 - 127
3X-RAY DIFFRACTION1AA159 - 207159 - 207
4X-RAY DIFFRACTION2AA36 - 8636 - 86
5X-RAY DIFFRACTION2AC - B301 - 302
6X-RAY DIFFRACTION3AA128 - 158128 - 158

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