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- PDB-8vij: Crystal structure of Shewanella benthica Group 1 truncated hemogl... -

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Basic information

Entry
Database: PDB / ID: 8vij
TitleCrystal structure of Shewanella benthica Group 1 truncated hemoglobin Y34F C51S C71S variant (cyanomet)
ComponentsGroup 1 truncated hemoglobin
KeywordsHEME-BINDING PROTEIN / GLOBIN / 2/2 HEMOGLOBIN / HEME BINDING PROTEIN / PSYCHROPIEZOPHILE
Function / homology
Function and homology information


oxygen transport / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin, bacterial-like, conserved site / Protozoan/cyanobacterial globins signature. / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globin-like superfamily
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Group 1 truncated hemoglobin
Similarity search - Component
Biological speciesShewanella benthica KT99 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.35 Å
AuthorsLecomte, J.T.J. / Schlessman, J.L. / Martinez, J.E. / Schultz, T.D. / Siegler, M.A. / DelCampo, M. / Le Magueres, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2003950 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Extremophilic hemoglobins: The structure of Shewanella benthica truncated hemoglobin N.
Authors: Martinez Grundman, J.E. / Schultz, T.D. / Schlessman, J.L. / Johnson, E.A. / Gillilan, R.E. / Lecomte, J.T.J.
History
DepositionJan 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group 1 truncated hemoglobin
B: Group 1 truncated hemoglobin
C: Group 1 truncated hemoglobin
D: Group 1 truncated hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,86012
Polymers51,2904
Non-polymers2,5708
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-108 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.464, 105.154, 151.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Group 1 truncated hemoglobin


Mass: 12822.427 Da / Num. of mol.: 4 / Mutation: Y34F, C51S, C71S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella benthica KT99 (bacteria) / Strain: KT99 / Gene: KT99_16901 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9DF82
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CN
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23% PEG MME 2000, 100 mM Bis-Tris pH 6.5, 10 mM KCN

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: Temperature oscillated and increased to about 105 K first and then 110 K in the last quarter of the experiment.
Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-Arc 100 / Detector: PIXEL / Date: Jul 3, 2022
RadiationMonochromator: Rigaku VariMax DW optics (confocal multilayer)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.35→18.97 Å / Num. obs: 97066 / % possible obs: 99 % / Redundancy: 5 % / Biso Wilson estimate: 7.83 Å2 / Rsym value: 0.081 / Net I/σ(I): 11.02
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.46 / Num. unique obs: 9662 / Rsym value: 0.286 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5072refinement
CrysalisProCrysAlisPro 42.64adata scaling
PHASER1.21rc1_5072phasing
CrysalisProCrysAlisPro 42.64adata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.35→16.97 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.8 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2012 1997 2.06 %
Rwork0.163 --
obs0.1638 96952 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→16.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3588 0 180 422 4190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054222
X-RAY DIFFRACTIONf_angle_d0.785825
X-RAY DIFFRACTIONf_dihedral_angle_d13.831731
X-RAY DIFFRACTIONf_chiral_restr0.071621
X-RAY DIFFRACTIONf_plane_restr0.006759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.21971410.19876680X-RAY DIFFRACTION98
1.38-1.420.2421390.17536639X-RAY DIFFRACTION99
1.42-1.460.21691420.16036717X-RAY DIFFRACTION99
1.46-1.510.20631410.14776739X-RAY DIFFRACTION100
1.51-1.560.19571420.14126726X-RAY DIFFRACTION100
1.56-1.630.19851440.13846834X-RAY DIFFRACTION100
1.63-1.70.17951430.14076764X-RAY DIFFRACTION100
1.7-1.790.19171420.14536774X-RAY DIFFRACTION100
1.79-1.90.18541430.15676816X-RAY DIFFRACTION100
1.9-2.050.20871440.15576834X-RAY DIFFRACTION100
2.05-2.250.1971440.1586845X-RAY DIFFRACTION100
2.25-2.580.22311400.16956664X-RAY DIFFRACTION96
2.58-3.250.19231380.18366628X-RAY DIFFRACTION95
3.25-16.970.19711540.17017295X-RAY DIFFRACTION100

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