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- PDB-1or4: Crystal Structure of HemAT sensor domain from B.subtilis in the c... -

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Basic information

Entry
Database: PDB / ID: 1or4
TitleCrystal Structure of HemAT sensor domain from B.subtilis in the cyano-liganded form
ComponentsHeme-based aerotactic transducer hemAT
KeywordsSIGNALING PROTEIN / Globin fold
Function / homology
Function and homology information


aerotaxis / oxygen binding / chemotaxis / heme binding / signal transduction / metal ion binding / membrane
Similarity search - Function
Protoglobin, globin sensor domain / Globin-sensor domain / Protoglobin / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / Globin/Protoglobin / Globins / Globin-like ...Protoglobin, globin sensor domain / Globin-sensor domain / Protoglobin / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Heme-based aerotactic transducer HemAT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsZhang, W. / Phillips Jr., G.N.
CitationJournal: Structure / Year: 2003
Title: Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry.
Authors: Zhang, W. / Phillips, G.N.
History
DepositionMar 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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: Heme-based aerotactic transducer hemAT
B: Heme-based aerotactic transducer hemAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9676
Polymers41,6822
Non-polymers1,2854
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-62 kcal/mol
Surface area13880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.994, 80.117, 85.944
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 Heme-based aerotactic transducer hemAT


Mass: 20841.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yhfV / Plasmid: pET29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O07621
#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium citrate, KH2PO4, n-Octyl-D-glucoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-18 %sodium citrate1reservoir
2100 mM1reservoirpH7.0KH2PO4
30.1 %n-octyl-beta-D-glucoside1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELMADMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→100 Å / Num. all: 31839 / Num. obs: 31839 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.15→2.23 Å / % possible all: 83.7
Reflection
*PLUS
Lowest resolution: 27 Å / Num. obs: 18722 / Num. measured all: 83301 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 83.7 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 5.35

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.15→26.98 Å / Num. parameters: 12286 / Num. restraintsaints: 12870 / Cross valid method: FREE R / σ(F): 0 / Details: ANISOTROPIC REFINEMENT APPLIED TO HEME GROUP ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 1379 4.3 %RANDOM
Rwork0.197 ---
obs0.197 31839 100 %-
all-31839 --
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Num. disordered residues: 4 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2901.5
Refinement stepCycle: LAST / Resolution: 2.15→26.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 90 204 2960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0.005
X-RAY DIFFRACTIONs_from_restr_planes0.0237
X-RAY DIFFRACTIONs_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.002
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.108
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 27 Å / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.324

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