[English] 日本語
Yorodumi
- PDB-3zxq: CRYSTAL STRUCTURE OF THE ATP-BINDING DOMAIN OF MYCOBACTERIUM TUBE... -

+
Open data


ID or keywords:

Loading...

-
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 / protein histidine kinase activity / carbon monoxide binding / nitric oxide binding / oxygen sensor activity / histidine kinase / phosphorelay sensor kinase activity / oxygen binding / protein autophosphorylation / membrane => GO:0016020 ...detection of hypoxia / protein histidine kinase activity / carbon monoxide binding / nitric oxide binding / oxygen sensor activity / histidine kinase / phosphorelay sensor kinase activity / oxygen binding / protein autophosphorylation / membrane => GO:0016020 / protein dimerization activity / protein kinase activity / calcium ion binding / heme binding / magnesium ion binding / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
GAF domain / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / GAF domain / 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 ...GAF domain / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / GAF domain / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more