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- PDB-1ux8: X-ray structure of truncated oxygen-avid haemoglobin from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 1ux8
TitleX-ray structure of truncated oxygen-avid haemoglobin from Bacillus subtilis
ComponentsYJBI PROTEIN
KeywordsOXYGEN STORAGE/TRANSPORT / TRUNCATED HEMOGLOBIN / OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT complex
Function / homology
Function and homology information


thioredoxin peroxidase activity / oxygen transport / cell redox homeostasis / oxygen binding / cellular response to oxidative stress / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Globin, bacterial-like, conserved site / Protozoan/cyanobacterial globins signature. / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Group 2 truncated hemoglobin YjbI
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsIlari, A. / Giangiacomo, L. / Boffi, A. / Chiancone, E.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The Truncated Oxygen-Avid Hemoglobin from Bacillus Subtilis: X-Ray Structure and Ligand Binding Properties
Authors: Giangiacomo, L. / Ilari, A. / Boffi, A. / Morea, V. / Chiancone, E.
History
DepositionFeb 20, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YJBI PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8134
Polymers15,1351
Non-polymers6783
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.193, 41.193, 134.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein YJBI PROTEIN / TRUNCATED HEMOGLOBIN


Mass: 15135.085 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31607
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.2 Å3/Da / Density % sol: 43.6 %
Crystal growpH: 6
Details: 2,0 M AMMONIUM SULFATE, 5% V/V ISOPROPANOL, PH=6.0, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 6975 / % possible obs: 98.6 % / Redundancy: 4 % / Biso Wilson estimate: 22.95 Å2 / Rmerge(I) obs: 0.098

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NGK

1ngk


Resolution: 2.15→39.5 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.261 323 4.8 %RANDOM
Rwork0.206 ---
obs0.208 6442 98.7 %-
Displacement parametersBiso mean: 22.16 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 46 77 1079

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