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- PDB-2y8h: STRUCTURE OF THE FIRST GAF DOMAIN E87G MUTANT OF MYCOBACTERIUM TU... -

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Basic information

Entry
Database: PDB / ID: 2y8h
TitleSTRUCTURE OF THE FIRST GAF DOMAIN E87G MUTANT OF MYCOBACTERIUM TUBERCULOSIS DOSS
ComponentsTWO COMPONENT SENSOR HISTIDINE KINASE DEVS
KeywordsTRANSFERASE
Function / homology
Function and homology information


detection of redox state / detection of hypoxia / carbon monoxide binding / nitric oxide binding / oxygen sensor activity / response to redox state / phosphorelay sensor kinase activity / histidine kinase / peptidoglycan-based cell wall / oxygen binding ...detection of redox state / detection of hypoxia / carbon monoxide binding / nitric oxide binding / oxygen sensor activity / response to redox state / phosphorelay sensor kinase activity / histidine kinase / peptidoglycan-based cell wall / oxygen binding / protein kinase activity / protein dimerization activity / heme binding / magnesium ion binding / ATP binding / membrane / 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 / GAF domain / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / 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 / GAF domain / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 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
PROTOPORPHYRIN IX CONTAINING FE / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCho, H.Y. / Cho, H.J. / Kang, B.S.
CitationJournal: FEBS Lett. / Year: 2011
Title: Blockage of the Channel to Heme by the E87 Side Chain in the Gaf Domain of Mycobacterium Tuberculosis Doss Confers the Unique Sensitivity of Doss to Oxygen.
Authors: Cho, H.Y. / Cho, H.J. / Kim, M.H. / Kang, B.S.
History
DepositionFeb 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry / _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: TWO COMPONENT SENSOR HISTIDINE KINASE DEVS
B: TWO COMPONENT SENSOR HISTIDINE KINASE DEVS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6415
Polymers33,3682
Non-polymers1,2733
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-67.3 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.740, 86.764, 100.459
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 TWO COMPONENT SENSOR HISTIDINE KINASE DEVS / TWO COMPONENT SENSOR HISTIDINE KINASE DOSS


Mass: 16683.932 Da / Num. of mol.: 2 / Fragment: GAF DOMAIN, RESIDUES 63-210 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: D63 TO K210 OF DOSS WITH ADDITIONAL GAMDP / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5U7E7, UniProt: P9WGK3*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsD63 TO K210 OF DOSS WITH ADDITIONAL GAMDP SEQUENCE AT THE N-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: 2.4 Å3/Da / Density % sol: 48.84 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 17% PEG 3350, 200 MM CALCIUM ACETATE, 100 MM TRIS-HCL, PH 7.0

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.99999
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25905 / % possible obs: 99 % / Observed criterion σ(I): -2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.4 / % possible all: 86.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W3D

2w3d


Resolution: 1.9→31.24 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.635 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25585 1313 5.1 %RANDOM
Rwork0.20988 ---
obs0.21226 24411 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 87 308 2672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4282.0773404
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4955308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65522.736106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1615361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0551521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211929
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_it0.8171.51510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41522437
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0033961
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1524.5962
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
Rfree0.37 93 -
Rwork0.33 1560 -
obs--87.28 %

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