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- PDB-1znw: Crystal Structure Of Unliganded Form Of Mycobacterium tuberculosi... -

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Basic information

Entry
Database: PDB / ID: 1znw
TitleCrystal Structure Of Unliganded Form Of Mycobacterium tuberculosis Guanylate Kinase
ComponentsGuanylate kinase
KeywordsTRANSFERASE / Guanylate kinase / GMP kinase / ATP:GMP-phosphotransferase
Function / homology
Function and homology information


guanylate kinase / GMP kinase activity / AMP kinase activity / GMP binding / GDP binding / magnesium ion binding / ATP binding / cytoplasm / 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
Guanylate kinase / Guanylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHible, G. / Christova, P. / Renault, L. / Seclaman, E. / Thompson, A. / Girard, E. / Munier-Lehmann, H. / Cherfils, J.
CitationJournal: Proteins / Year: 2006
Title: Unique GMP-binding site in Mycobacterium tuberculosis guanosine monophosphate kinase
Authors: Hible, G. / Christova, P. / Renault, L. / Seclaman, E. / Thompson, A. / Girard, E. / Munier-Lehmann, H. / Cherfils, J.
History
DepositionMay 12, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanylate kinase


Theoretical massNumber of molelcules
Total (without water)21,9911
Polymers21,9911
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.040, 112.040, 112.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-250-

HOH

21A-271-

HOH

DetailsThe biological unit is monomeric

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Components

#1: Protein Guanylate kinase / GMP kinase


Mass: 21991.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: gmk (RV1389) / Plasmid: pET22b / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5I4, UniProt: P9WKE9*PLUS, guanylate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 15% (w/v) xylitol, 3.5M sodium chloride, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2003 / Details: mirrors
RadiationMonochromator: Si(311) monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.1→18.67 Å / Num. all: 13765 / Num. obs: 13765 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.8 % / Biso Wilson estimate: 44.8 Å2 / Rsym value: 0.059 / Net I/σ(I): 32.7
Reflection shellResolution: 2.1→2.154 Å / Redundancy: 22 % / Mean I/σ(I) obs: 8.2 / Num. unique all: 1028 / Rsym value: 0.451 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
XSCALEdata scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S4Q

1s4q


Resolution: 2.1→18.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.658 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21976 693 5 %RANDOM
Rwork0.19209 ---
obs0.19346 13049 99.71 %-
all-13778 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.749 Å2
Refinement stepCycle: LAST / Resolution: 2.1→18.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 0 67 1452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221409
X-RAY DIFFRACTIONr_bond_other_d0.0020.021361
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9681918
X-RAY DIFFRACTIONr_angle_other_deg0.80133131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4845181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1322.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74315232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3041517
X-RAY DIFFRACTIONr_chiral_restr0.1010.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021060
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02286
X-RAY DIFFRACTIONr_nbd_refined0.1990.2549
X-RAY DIFFRACTIONr_nbd_other0.2360.21456
X-RAY DIFFRACTIONr_nbtor_refined0.30.2967
X-RAY DIFFRACTIONr_nbtor_other0.0810.2878
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2191.5927
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35221462
X-RAY DIFFRACTIONr_scbond_it2.6863530
X-RAY DIFFRACTIONr_scangle_it4.2394.5456
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 52 -
Rwork0.217 940 -
obs-1028 99.9 %
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)
12.4001-1.8434-0.72173.00720.32693.9246-0.19960.0801-0.01460.13280.06760.0881-0.2259-0.09010.1320.1102-0.0391-0.00380.07290.01440.102317.6970.66842.407
27.00941.2610.51743.4157-1.44583.2999-0.01820.4998-0.1212-0.446-0.1612-0.19450.27920.02790.17940.1449-0.02030.02740.14920.02330.064927.1611.22824.866
32.67650.8231-0.05486.7356-0.08313.45960.12710.0452-0.1062-0.1565-0.0606-0.16660.02950.2462-0.06640.1230.0945-0.01080.1030.03060.049515.66822.89240.962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA20 - 5019 - 49
2X-RAY DIFFRACTION1AA102 - 140101 - 139
3X-RAY DIFFRACTION1AA180 - 201179 - 200
4X-RAY DIFFRACTION2AA51 - 10150 - 100
5X-RAY DIFFRACTION3AA141 - 179140 - 178

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