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- PDB-5jrv: Crystal structure of Fe(II) NO-bound H-NOX protein from C. subter... -

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Basic information

Entry
Database: PDB / ID: 5jrv
TitleCrystal structure of Fe(II) NO-bound 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


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 / IODIDE ION / NITRIC OXIDE / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.953 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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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)45,5157
Polymers44,0952
Non-polymers1,4205
Water4,882271
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A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6943
Polymers22,0481
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8214
Polymers22,0481
Non-polymers7733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.385, 127.626, 42.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 22047.502 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.6 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Anaerobically grown under Argon. 20 mg/mL protein with well condition of 0.15 M NaI, 25% PEG3350.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999919 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 32785 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.5 Å2 / CC1/2: 0.909 / Rmerge(I) obs: 0.093 / Rsym value: 0.087 / Net I/σ(I): 14.9
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.67 / % 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: 1.953→49.979 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1585 4.85 %
Rwork0.2016 --
obs0.2031 32689 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.953→49.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 91 271 3462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043271
X-RAY DIFFRACTIONf_angle_d0.784410
X-RAY DIFFRACTIONf_dihedral_angle_d14.9471948
X-RAY DIFFRACTIONf_chiral_restr0.044452
X-RAY DIFFRACTIONf_plane_restr0.004550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.953-2.0160.2931220.24782631X-RAY DIFFRACTION94
2.016-2.08810.25251410.24662783X-RAY DIFFRACTION100
2.0881-2.17170.28731420.22592822X-RAY DIFFRACTION100
2.1717-2.27050.28581390.26492800X-RAY DIFFRACTION99
2.2705-2.39030.24291480.22062806X-RAY DIFFRACTION100
2.3903-2.540.2491580.21642791X-RAY DIFFRACTION100
2.54-2.73610.23241460.21262821X-RAY DIFFRACTION100
2.7361-3.01140.24551390.21512868X-RAY DIFFRACTION100
3.0114-3.44710.23851710.20472818X-RAY DIFFRACTION100
3.4471-4.34260.20161230.18262941X-RAY DIFFRACTION100
4.3426-49.99570.20921560.17783023X-RAY DIFFRACTION99

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