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- PDB-3lah: Structural insights into the molecular mechanism of H-NOX activation -

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Basic information

Entry
Database: PDB / ID: 3lah
TitleStructural insights into the molecular mechanism of H-NOX activation
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


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 / IMIDAZOLE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOlea Jr, C. / Herzik Jr, M.A. / Kuriyan, J. / Marletta, M.A.
CitationJournal: Protein Sci. / Year: 2010
Title: Structural insights into the molecular mechanism of H-NOX activation.
Authors: Olea, C. / Herzik, M.A. / Kuriyan, J. / Marletta, M.A.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4428
Polymers43,9332
Non-polymers1,5096
Water2,648147
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7214
Polymers21,9661
Non-polymers7553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7214
Polymers21,9661
Non-polymers7553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.353, 88.713, 89.207
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 Methyl-accepting chemotaxis protein


Mass: 21966.406 Da / Num. of mol.: 2 / Fragment: UNP residues 1-188 / Mutation: H102G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Gene: Tar4, TTE0680 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RBX6
#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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% (w/v) PEG 3350, 0.25 M magnesium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2009
RadiationMonochromator: Asymmetric Curved Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2→44.6 Å / Num. obs: 62250 / % possible obs: 97.5 %
Reflection shellResolution: 2→2.07 Å / % possible all: 80.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.6 Å / SU ML: 0.31 / σ(F): 1.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 1684 5.08 %random
Rwork0.2151 ---
obs0.217 33172 51.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.554 Å2 / ksol: 0.344 e/Å3
Refinement stepCycle: LAST / Resolution: 2→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 106 147 3343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083272
X-RAY DIFFRACTIONf_angle_d0.8674414
X-RAY DIFFRACTIONf_dihedral_angle_d17.1851230
X-RAY DIFFRACTIONf_chiral_restr0.061450
X-RAY DIFFRACTIONf_plane_restr0.003554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9909-2.04940.32711140.26082057X-RAY DIFFRACTION40
2.0494-2.11560.30911450.24682473X-RAY DIFFRACTION49
2.1156-2.19120.26991510.22322591X-RAY DIFFRACTION51
2.1912-2.27890.26871410.2232637X-RAY DIFFRACTION52
2.2789-2.38270.25891300.22482677X-RAY DIFFRACTION52
2.3827-2.50830.31121330.24352684X-RAY DIFFRACTION52
2.5083-2.66540.32631270.23772689X-RAY DIFFRACTION52
2.6654-2.87120.29771460.23772664X-RAY DIFFRACTION53
2.8712-3.160.26671500.23482697X-RAY DIFFRACTION53
3.16-3.61710.25961470.22482714X-RAY DIFFRACTION53
3.6171-4.55650.20791460.18372723X-RAY DIFFRACTION54
4.5565-44.61470.20491540.192882X-RAY DIFFRACTION56

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