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- PDB-1s4q: Crystal Structure of Guanylate Kinase from Mycobacterium tubercul... -

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Basic information

Entry
Database: PDB / ID: 1s4q
TitleCrystal Structure of Guanylate Kinase from Mycobacterium tuberculosis (Rv1389)
ComponentsGuanylate kinase
KeywordsTRANSFERASE / ATP:GMP-phosphotransferase / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


GMP binding / guanylate kinase / guanylate kinase activity / adenylate kinase activity / GDP binding / phosphorylation / magnesium ion binding / ATP binding / cytosol / cytoplasm
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Guanylate kinase / Guanylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.16 Å
AuthorsChan, S. / Sawaya, M.R. / Perry, L.J. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal Structure of Guanylate Kinase from Mycobacterium tuberculosis
Authors: Chan, S. / Sawaya, M.R. / Perry, L.J. / Eisenberg, D.
History
DepositionJan 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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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)24,4605
Polymers24,2871
Non-polymers1744
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.126, 112.126, 112.126
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-336-

HOH

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Components

#1: Protein Guanylate kinase / / GMP kinase


Mass: 24286.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: GMK, RV1389, MT1434, MTCY21B4.06, MB1424 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)
References: UniProt: P0A5I4, UniProt: P9WKE9*PLUS, guanylate kinase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: sodium formate, glycerol, Tris, sodium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 5, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.16→79.06 Å / Num. all: 12112 / Num. obs: 12112 / % possible obs: 99.91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.91 % / Rsym value: 0.058 / Net I/σ(I): 36.6
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 4.94 / Num. unique all: 1270 / Rsym value: 0.508 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.16→79.06 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.513 / SU ML: 0.118 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.197 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23071 642 5 %RANDOM
Rwork0.17717 ---
all0.17988 12112 --
obs0.17988 12112 99.91 %-
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: 36.464 Å2
Refinement stepCycle: LAST / Resolution: 2.16→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 10 134 1533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0211419
X-RAY DIFFRACTIONr_bond_other_d0.0040.021367
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9631926
X-RAY DIFFRACTIONr_angle_other_deg0.98733144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9255182
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_restr0.1290.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021580
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02287
X-RAY DIFFRACTIONr_nbd_refined0.2160.2282
X-RAY DIFFRACTIONr_nbd_other0.2560.21542
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.2861
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2011.5915
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17321467
X-RAY DIFFRACTIONr_scbond_it3.4353504
X-RAY DIFFRACTIONr_scangle_it5.9234.5459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.159→2.216 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.234 46
Rwork0.216 893

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