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- PDB-5jrx: Crystal structure of Fe(II) CO-bound H-NOX protein from C. subter... -

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Basic information

Entry
Database: PDB / ID: 5jrx
TitleCrystal structure of Fe(II) CO-bound H-NOX protein from C. subterraneus
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / Heme-based methyl-accepting chemotaxis protein / Gas binding
Function / homology
Function and homology information


heme binding / signal transduction / metal ion binding / membrane
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBruegger, J. / Hespen, C. / Phillips-Piro, C.M. / Marletta, M.A.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structural and Functional Evidence Indicates Selective Oxygen Signaling in Caldanaerobacter subterraneus H-NOX.
Authors: Hespen, C.W. / Bruegger, J.J. / Phillips-Piro, C.M. / Marletta, M.A.
History
DepositionMay 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)45,3846
Polymers44,0952
Non-polymers1,2894
Water4,179232
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6923
Polymers22,0481
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6923
Polymers22,0481
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.865, 127.205, 42.699
Angle α, β, γ (deg.)90.00, 95.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyl-accepting chemotaxis protein


Mass: 22047.502 Da / Num. of mol.: 2 / Mutation: UNP residues 1-188
Source method: isolated from a genetically manipulated source
Details: Fragment: N-terminal Heme nitric oxide/oxygen binding protein (H-NOX) (UNP Residues 1-186)
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: Tar4, TTE0680 / Production host: Escherichia coli (E. coli) / Strain (production host): RP523 (DE3) / 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Anaerobically grown under Argon. 30 mg/mL protein with well condition 0.1 M LiCl, 20% PEG 3350.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2015
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 1.95→38.19 Å / Num. obs: 35087 / % possible obs: 99.9 % / Redundancy: 4.7 % / CC1/2: 0.871 / Rmerge(I) obs: 0.084 / Rsym value: 0.076 / Net I/σ(I): 14
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U55

1u55


Resolution: 1.95→38.187 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 1740 4.96 %
Rwork0.1862 --
obs0.1881 35051 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→38.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 90 232 3376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013228
X-RAY DIFFRACTIONf_angle_d1.0714349
X-RAY DIFFRACTIONf_dihedral_angle_d14.1791918
X-RAY DIFFRACTIONf_chiral_restr0.053447
X-RAY DIFFRACTIONf_plane_restr0.007543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00370.31951200.25892623X-RAY DIFFRACTION94
2.0037-2.06840.28941300.23552797X-RAY DIFFRACTION100
2.0684-2.14230.2611460.22652777X-RAY DIFFRACTION100
2.1423-2.22810.24511440.22672790X-RAY DIFFRACTION100
2.2281-2.32950.25051520.21822759X-RAY DIFFRACTION100
2.3295-2.45230.26011570.21652782X-RAY DIFFRACTION100
2.4523-2.60590.24911570.21752793X-RAY DIFFRACTION100
2.6059-2.80710.25711520.21072784X-RAY DIFFRACTION100
2.8071-3.08940.27591510.19492780X-RAY DIFFRACTION100
3.0894-3.53620.25271370.18652822X-RAY DIFFRACTION100
3.5362-4.45410.18171510.15912784X-RAY DIFFRACTION100
4.4541-38.19390.17151430.14922820X-RAY DIFFRACTION99

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