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- PDB-3zxq: CRYSTAL STRUCTURE OF THE ATP-BINDING DOMAIN OF MYCOBACTERIUM TUBE... -

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Basic information

Entry
Database: PDB / ID: 3zxq
TitleCRYSTAL STRUCTURE OF THE ATP-BINDING DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOST
ComponentsHYPOXIA SENSOR HISTIDINE KINASE RESPONSE REGULATOR DOST
KeywordsTRANSFERASE
Function / homology
Function and homology information


detection of hypoxia / carbon monoxide binding / protein histidine kinase activity / nitric oxide binding / oxygen sensor activity / phosphorelay sensor kinase activity / histidine kinase / membrane => GO:0016020 / oxygen binding / protein kinase activity ...detection of hypoxia / carbon monoxide binding / protein histidine kinase activity / nitric oxide binding / oxygen sensor activity / phosphorelay sensor kinase activity / histidine kinase / membrane => GO:0016020 / oxygen binding / protein kinase activity / protein dimerization activity / heme binding / calcium ion binding / magnesium ion binding / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
GAF domain / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / : / Histidine kinase / GAF domain / Histidine kinase/HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain ...GAF domain / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / : / Histidine kinase / GAF domain / Histidine kinase/HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Oxygen sensor histidine kinase response regulator DosT / Oxygen sensor histidine kinase response regulator DosT
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCho, H.Y. / Cho, H.J. / Kang, B.S.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: Activation of ATP Binding for the Autophosphorylation of Doss, a Mycobacterium Tuberculosis Histidine Kinase Lacking an ATP-Lid Motif.
Authors: Cho, H.Y. / Lee, Y.H. / Bae, Y.S. / Kim, E. / Kang, B.S.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: A Gaf Domain in the Hypoxia/No-Inducible Mycobacterium Tuberculosis Doss Protein Binds Haem.
Authors: Sardiwal, S. / Kendall, S.L. / Movahedzadeh, F. / Rison, S.C.G. / Stoker, N.G. / Djordjevic, S.
History
DepositionAug 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Derived calculations
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3May 22, 2013Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: HYPOXIA SENSOR HISTIDINE KINASE RESPONSE REGULATOR DOST
B: HYPOXIA SENSOR HISTIDINE KINASE RESPONSE REGULATOR DOST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5974
Polymers26,5262
Non-polymers712
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-38.9 kcal/mol
Surface area11850 Å2
MethodPISA
2
A: HYPOXIA SENSOR HISTIDINE KINASE RESPONSE REGULATOR DOST
hetero molecules

B: HYPOXIA SENSOR HISTIDINE KINASE RESPONSE REGULATOR DOST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5974
Polymers26,5262
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
Buried area1920 Å2
ΔGint-27.6 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.914, 65.867, 72.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HYPOXIA SENSOR HISTIDINE KINASE RESPONSE REGULATOR DOST / TWO COMPONENT SENSOR HISTIDINE KINASE


Mass: 13262.812 Da / Num. of mol.: 2 / Fragment: ATP-BINDING DOMAIN, RESIDUES 451-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53473, UniProt: P9WGK1*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsT451 TO Q573 OF DOSS WITH ADDITIONAL L SEQUENCE AT THE C- TERMINUS DUE TO CLONING PROCEDURE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.2 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1.5 M SODIUM CHLORIDE, 10% ETHANOL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 37177 / % possible obs: 99.7 % / Observed criterion σ(I): -2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.95
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.18 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZXO

3zxo


Resolution: 1.9→31.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.121 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23163 1016 5.1 %RANDOM
Rwork0.19416 ---
obs0.19605 18850 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.349 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 2 144 2000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211948
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9542677
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.865267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69723.37189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80115318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1391522
X-RAY DIFFRACTIONr_chiral_restr0.0940.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211483
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
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_it0.8461.51257
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5522048
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3563691
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0364.5617
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 73 -
Rwork0.21 1364 -
obs--99.65 %

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