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- PDB-4u9b: Crystal structure of an H-NOX protein from S. oneidensis in the F... -

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Basic information

Entry
Database: PDB / ID: 4u9b
TitleCrystal structure of an H-NOX protein from S. oneidensis in the Fe(II)NO ligation state
ComponentsNO-binding heme-dependent sensor protein
KeywordsSIGNALING PROTEIN / H-NOX / hemoprotein / gas sensor
Function / homology
Function and homology information


heme binding / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / PHOSPHATE ION / NO-binding heme-dependent sensor protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHerzik Jr., M.A. / Jonnalagadda, R. / Kuriyan, J. / Marletta, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association11PRE7370086 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural insights into the role of iron-histidine bond cleavage in nitric oxide-induced activation of H-NOX gas sensor proteins.
Authors: Herzik, M.A. / Jonnalagadda, R. / Kuriyan, J. / Marletta, M.A.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NO-binding heme-dependent sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2286
Polymers21,3291
Non-polymers8995
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.636, 86.716, 33.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NO-binding heme-dependent sensor protein


Mass: 21329.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_2144 / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / Strain (production host): RP523(DE3) / References: UniProt: Q8EF49

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Non-polymers , 6 types, 126 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Obtained by equilibrating a 2 or 4 uL drop of 1:1 protein: reservoir against 700 uL reservoir containing 0.7 M NaH2PO4, 0.9 M K2HPO4. Cryoprotection was achieved by carefully adding equal ...Details: Obtained by equilibrating a 2 or 4 uL drop of 1:1 protein: reservoir against 700 uL reservoir containing 0.7 M NaH2PO4, 0.9 M K2HPO4. Cryoprotection was achieved by carefully adding equal drop volume of mother liquor containing 50% glycerol. Crystals were then transferred into mother liquor containing 30% glycerol and flash frozen in liquid nitrogen. All crystal growth and manipulation was performed anaerobically.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.65→33.818 Å / Num. all: 45550 / Num. obs: 45550 / % possible obs: 98.46 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 14.4
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.7 / % possible all: 99.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U99

4u99


Resolution: 1.65→33.818 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2027 2302 5.05 %
Rwork0.1675 --
obs0.1693 45550 98.46 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→33.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 57 121 1608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191543
X-RAY DIFFRACTIONf_angle_d0.8642092
X-RAY DIFFRACTIONf_dihedral_angle_d13.749557
X-RAY DIFFRACTIONf_chiral_restr0.029223
X-RAY DIFFRACTIONf_plane_restr0.003266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.68590.38771340.33032591X-RAY DIFFRACTION94
1.6859-1.72510.31971950.30372672X-RAY DIFFRACTION99
1.7251-1.76830.27921320.26532761X-RAY DIFFRACTION99
1.7683-1.81610.3021160.24552716X-RAY DIFFRACTION99
1.8161-1.86950.26651330.22232743X-RAY DIFFRACTION99
1.8695-1.92980.24011330.19292721X-RAY DIFFRACTION99
1.9298-1.99880.22431440.18712755X-RAY DIFFRACTION99
1.9988-2.07880.18291170.17532756X-RAY DIFFRACTION99
2.0788-2.17340.20141530.1592680X-RAY DIFFRACTION99
2.1734-2.2880.22191350.1572740X-RAY DIFFRACTION99
2.288-2.43130.20651440.14892735X-RAY DIFFRACTION99
2.4313-2.61890.18461610.15042710X-RAY DIFFRACTION99
2.6189-2.88240.17961530.15342668X-RAY DIFFRACTION99
2.8824-3.29920.18681380.15212689X-RAY DIFFRACTION97
3.2992-4.15540.17221480.14542657X-RAY DIFFRACTION97
4.1554-33.82510.19231660.15512654X-RAY DIFFRACTION98

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