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- PDB-1xbn: Crystal structure of a bacterial nitric oxide sensor: an ortholog... -

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Basic information

Entry
Database: PDB / ID: 1xbn
TitleCrystal structure of a bacterial nitric oxide sensor: an ortholog of mammalian soluble guanylate cyclase heme domain
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsSIGNALING PROTEIN / SOLUBLE GUANYLYL CYCLASE / NITRIC OXIDE / HEME PROTEIN / CGMP
Function / homology
Function and homology information


lysozyme activity / heme binding / signal transduction / membrane / metal ion binding
Similarity search - Function
H-NOX domain / H-NOX domain / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / 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). ...H-NOX domain / H-NOX domain / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / 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). / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis MB4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsNioche, P. / Raman, C.S.
CitationJournal: Science / Year: 2004
Title: Femtomolar sensitivity of a NO sensor from Clostridium botulinum
Authors: Nioche, P. / Berka, V. / Vipond, J. / Minton, N. / Tsai, A.-L. / Raman, C.S.
History
DepositionAug 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ref_seq_dif.details / _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: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5053
Polymers22,8561
Non-polymers6482
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.607, 120.607, 120.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232

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Components

#1: Protein Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins


Mass: 22856.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis MB4 (bacteria)
Species: Thermoanaerobacter tengcongensis / Strain: MB4T / Gene: Tar4 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RBX6
#2: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.25 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: MPD, cacodylate, pH 6, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.7403,1.7379,1.6241,1.1159
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2003
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.74031
21.73791
31.62411
41.11591
ReflectionResolution: 2.5→85 Å / Num. all: 10884 / Num. obs: 10884 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11 % / Biso Wilson estimate: 87 Å2 / Rsym value: 0.057 / Net I/σ(I): 41
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.67 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→84.51 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.616 / SU ML: 0.266 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.433 / ESU R Free: 0.294
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BUSTER-TNT (AUTHOR: G.BRICOGNE) WAS ALSO USED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.29147 523 4.8 %RANDOM
Rwork0.2634 ---
all0.2647 10841 --
obs0.26471 10318 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.135 Å2
Refinement stepCycle: LAST / Resolution: 2.5→84.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 45 11 1665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0231643
X-RAY DIFFRACTIONr_bond_other_d0.0011500
X-RAY DIFFRACTIONr_angle_refined_deg1.9912229
X-RAY DIFFRACTIONr_angle_other_deg0.8713472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.121230
X-RAY DIFFRACTIONr_gen_planes_refined0.0211807
X-RAY DIFFRACTIONr_gen_planes_other0.007345
X-RAY DIFFRACTIONr_nbd_refined0.331522
X-RAY DIFFRACTIONr_nbd_other0.2921971
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1051036
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.28362
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2562
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.16712
X-RAY DIFFRACTIONr_symmetry_vdw_other0.29434
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0564
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.573970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8111558
X-RAY DIFFRACTIONr_scbond_it4.885673
X-RAY DIFFRACTIONr_scangle_it7.833671
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.72110.0056-0.00124.58390.74314.0555-0.0562-0.87720.45911.90360.3065-0.9605-0.23190.2567-0.25040.95960.145-0.22830.76860.07350.504687.18956.55425.726
29.6450.8632-1.1963.18091.0122.28310.0179-0.9599-0.18140.95290.15130.39710.05490.0673-0.16920.22060.1210.03250.37680.20390.116469.44454.3514.84
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 95
2X-RAY DIFFRACTION2A96 - 195

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