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- PDB-3zxo: CRYSTAL STRUCTURE OF THE MUTANT ATP-BINDING DOMAIN OF MYCOBACTERI... -

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Basic information

Entry
Database: PDB / ID: 3zxo
TitleCRYSTAL STRUCTURE OF THE MUTANT ATP-BINDING DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOSS
ComponentsREDOX SENSOR HISTIDINE KINASE RESPONSE REGULATOR DEVS
KeywordsTRANSFERASE
Function / homology
Function and homology information


detection of redox state / detection of hypoxia / carbon monoxide binding / nitric oxide binding / response to redox state / oxygen sensor activity / phosphorelay sensor kinase activity / histidine kinase / membrane => GO:0016020 / peptidoglycan-based cell wall ...detection of redox state / detection of hypoxia / carbon monoxide binding / nitric oxide binding / response to redox state / oxygen sensor activity / phosphorelay sensor kinase activity / histidine kinase / membrane => GO:0016020 / peptidoglycan-based cell wall / oxygen binding / protein kinase activity / protein dimerization activity / heme binding / magnesium ion binding / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / : / Histidine kinase / GAF domain / Histidine kinase/HSP90-like ATPase / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Domain present in phytochromes and cGMP-specific phosphodiesterases. ...Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / : / Histidine kinase / GAF domain / Histidine kinase/HSP90-like ATPase / Histidine kinase domain / Histidine kinase domain profile. / 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
ACETATE ION / Oxygen sensor histidine kinase response regulator DevS/DosS / Oxygen sensor histidine kinase response regulator DevS/DosS
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 13, 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 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: REDOX SENSOR HISTIDINE KINASE RESPONSE REGULATOR DEVS
B: REDOX SENSOR HISTIDINE KINASE RESPONSE REGULATOR DEVS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8939
Polymers27,4342
Non-polymers4597
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint0.9 kcal/mol
Surface area15000 Å2
MethodPISA
2
B: REDOX SENSOR HISTIDINE KINASE RESPONSE REGULATOR DEVS
hetero molecules

A: REDOX SENSOR HISTIDINE KINASE RESPONSE REGULATOR DEVS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8939
Polymers27,4342
Non-polymers4597
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_564y+1/2,-x+3/2,z-1/41
Buried area3090 Å2
ΔGint-84.5 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.186, 53.186, 184.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2048-

HOH

21A-2060-

HOH

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Components

#1: Protein REDOX SENSOR HISTIDINE KINASE RESPONSE REGULATOR DEVS / TWO COMPONENT SENSOR HISTIDINE KINASE DEVS


Mass: 13716.783 Da / Num. of mol.: 2 / Fragment: ATP-BINDING DOMAIN, RESIDUES 454-578 / Mutation: YES
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): B834
References: UniProt: P95194, UniProt: P9WGK3*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor, histidine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 509 TO ALA ENGINEERED RESIDUE IN CHAIN A, LEU 534 TO MET ...ENGINEERED RESIDUE IN CHAIN A, LYS 509 TO ALA ENGINEERED RESIDUE IN CHAIN A, LEU 534 TO MET ENGINEERED RESIDUE IN CHAIN A, VAL 562 TO MET ENGINEERED RESIDUE IN CHAIN B, LYS 509 TO ALA ENGINEERED RESIDUE IN CHAIN B, LEU 534 TO MET ENGINEERED RESIDUE IN CHAIN B, VAL 562 TO MET
Has protein modificationY
Sequence detailsADDITIONAL GAMV SEQUENCE AT THE N-TERMINUS DUE TO CLONING PROCEDURE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 % / Description: NONE
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 15% PEG 1500, 200 MM ZINC ACETATE, 100 MM CITRATE, PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.97908
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Jan 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25671 / % possible obs: 99.9 % / Observed criterion σ(I): -2 / Redundancy: 22.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 55.97
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 20.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 8.26 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→46.08 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.303 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. T454 TO Q578 OF DOSS WITH ADDITIONAL V SEQUENCE AT THE N- -TERMINUS DUE TO CLONING PROCEDURE
RfactorNum. reflection% reflectionSelection details
Rfree0.23585 1093 5.2 %RANDOM
Rwork0.1858 ---
obs0.18832 20025 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.668 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 24 190 2063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222018
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9662763
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2555284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44522.80989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8515331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3141526
X-RAY DIFFRACTIONr_chiral_restr0.1030.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211558
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_it1.0231.51324
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81822125
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7993694
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5974.5623
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
Rfree0.27 73 -
Rwork0.206 1354 -
obs--100 %

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