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- PDB-2y79: STRUCTURE OF THE FIRST GAF DOMAIN E87A MUTANT OF MYCOBACTERIUM TU... -

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Basic information

Entry
Database: PDB / ID: 2y79
TitleSTRUCTURE OF THE FIRST GAF DOMAIN E87A MUTANT 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 / oxygen sensor activity / response to redox state / 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 / oxygen sensor activity / response to redox state / 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 / GAF domain / Histidine kinase/HSP90-like ATPase / 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 / GAF domain / Histidine kinase/HSP90-like ATPase / 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: 1.8 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
DepositionJan 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr1_symmetry / _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

Downloads & links

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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)34,7616
Polymers33,3962
Non-polymers1,3654
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-69.2 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.932, 86.913, 100.973
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 REDOX SENSOR HISTIDINE KINASE RESPONSE REGULATOR DEVS / TWO COMPONENT SENSOR HISTIDINE KINASE DOSS


Mass: 16697.957 Da / Num. of mol.: 2 / Fragment: RESIDUES 63-210 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P95194, UniProt: P9WGK3*PLUS, histidine kinase
#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: 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.: 219 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 87 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 87 TO ALA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 7
Details: 19% PEG 6000, 200 MM CALCIUM ACETATE, 100 MM TRIS PH 7.0.

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2399
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 29661 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 32.3
Reflection shellResolution: 1.8→31.4 Å / Redundancy: 6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.3 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W3D

2w3d


Resolution: 1.8→31.39 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.866 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24808 1497 5.1 %RANDOM
Rwork0.19658 ---
obs0.19913 28098 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.518 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 93 219 2592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222454
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4912.0793376
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22522.963108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28515361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9081521
X-RAY DIFFRACTIONr_chiral_restr0.1050.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021915
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21203
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21703
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2189
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2460.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0610.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0621.51519
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7922401
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.42931037
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.684.5968
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 112 -
Rwork0.273 1769 -
obs--86.28 %

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