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- PDB-5jru: Crystal structure of Fe(II) unliganded H-NOX protein from C. subt... -

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Basic information

Entry
Database: PDB / ID: 5jru
TitleCrystal structure of Fe(II) unliganded H-NOX protein from C. subterraneus
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsSIGNALING PROTEIN / Heme-based methyl-accepting chemotaxis protein Gas binding Signaling 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 / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 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
C: Methyl-accepting chemotaxis protein
D: Methyl-accepting chemotaxis protein
E: Methyl-accepting chemotaxis protein
F: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,98412
Polymers132,2856
Non-polymers3,6996
Water7,837435
1
A: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
F: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9926
Polymers66,1433
Non-polymers1,8493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-115 kcal/mol
Surface area24910 Å2
MethodPISA
2
C: Methyl-accepting chemotaxis protein
D: Methyl-accepting chemotaxis protein
E: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9926
Polymers66,1433
Non-polymers1,8493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-115 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.264, 70.446, 108.419
Angle α, β, γ (deg.)90.00, 104.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 22047.502 Da / Num. of mol.: 6 / Fragment: UNP residues 1-188
Source method: isolated from a genetically manipulated source
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Anaerobically grown under Argon. 30 mg/mL protein with well condition of 0.1 M NaI, 22% PEG 3350.

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Under liquid nitrogen cryostream
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99994 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2014
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 2.3→44.92 Å / Num. obs: 55562 / % possible obs: 99.7 % / Redundancy: 2.01 % / Biso Wilson estimate: 28.6 Å2 / CC1/2: 0.968 / Rsym value: 0.18 / Net I/σ(I): 17.12
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 4.8 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LAH

3lah


Resolution: 2.305→44.919 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07
RfactorNum. reflection% reflection
Rfree0.2544 1997 3.59 %
Rwork0.1916 --
obs0.1938 55562 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.305→44.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9186 0 258 435 9879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149683
X-RAY DIFFRACTIONf_angle_d1.64613080
X-RAY DIFFRACTIONf_dihedral_angle_d14.8973680
X-RAY DIFFRACTIONf_chiral_restr0.0661343
X-RAY DIFFRACTIONf_plane_restr0.0081630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3049-2.36250.31991350.23193615X-RAY DIFFRACTION95
2.3625-2.42640.30131440.2263834X-RAY DIFFRACTION100
2.4264-2.49780.27121410.20863803X-RAY DIFFRACTION100
2.4978-2.57840.2931430.20723819X-RAY DIFFRACTION100
2.5784-2.67050.28181420.20933795X-RAY DIFFRACTION100
2.6705-2.77740.29131430.20983848X-RAY DIFFRACTION100
2.7774-2.90380.27811410.20273785X-RAY DIFFRACTION100
2.9038-3.05690.25641430.2063849X-RAY DIFFRACTION100
3.0569-3.24840.32481430.20033832X-RAY DIFFRACTION100
3.2484-3.49910.23361450.19893858X-RAY DIFFRACTION100
3.4991-3.8510.26431420.18443831X-RAY DIFFRACTION100
3.851-4.40790.20971440.16893850X-RAY DIFFRACTION100
4.4079-5.55180.2151440.16993885X-RAY DIFFRACTION100
5.5518-44.92790.22661470.17743961X-RAY DIFFRACTION100

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