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- PDB-2oif: The crystal structure of ferric cyanide bound barley hexacoordina... -

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Basic information

Entry
Database: PDB / ID: 2oif
TitleThe crystal structure of ferric cyanide bound barley hexacoordinate hemoglobin.
ComponentsNon-legume hemoglobin
KeywordsMETAL BINDING PROTEIN / hexacoordinate hemoglobin / barley / ligand binding / non-symbiotic / symbiotic / evolution / conformational changes / oxygen transport
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors; With a cytochrome as acceptor / oxygen binding / oxidoreductase activity / heme binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily ...Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / S-1,2-PROPANEDIOL / Anaerobic nitrite reductase GLB1
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 Å
AuthorsHoy, J.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Plant hemoglobins: a molecular fossil record for the evolution of oxygen transport
Authors: Hoy, J.A. / Robinson, H. / Trent III, J.T. / Kakar, S. / Smagghe, B.J. / Hargrove, M.S.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 19, 2017Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_distant_solvent_atoms ...database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Non-legume hemoglobin
B: Non-legume hemoglobin
C: Non-legume hemoglobin
D: Non-legume hemoglobin
E: Non-legume hemoglobin
F: Non-legume hemoglobin
G: Non-legume hemoglobin
H: Non-legume hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,67337
Polymers144,5448
Non-polymers6,12929
Water15,781876
1
A: Non-legume hemoglobin
F: Non-legume hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,72510
Polymers36,1362
Non-polymers1,5898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-legume hemoglobin
D: Non-legume hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6499
Polymers36,1362
Non-polymers1,5137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Non-legume hemoglobin
H: Non-legume hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6499
Polymers36,1362
Non-polymers1,5137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Non-legume hemoglobin
E: Non-legume hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6499
Polymers36,1362
Non-polymers1,5137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.740, 60.557, 145.804
Angle α, β, γ (deg.)99.17, 96.97, 92.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Non-legume hemoglobin / HORvu GLB1


Mass: 18068.020 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Gene: HB, GLB1 / Plasmid: pet29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q42831
#2: Chemical
ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CN
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 876 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 20% PEG 3350, 0.2 M ammonium citrate, 4% polypropylene glycol, 0.1 M sodium cyanide, 0.01 M hepes, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 141630 / Num. obs: 123785 / % possible obs: 87.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.378 / % possible all: 47.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24958 6195 5 %RANDOM
Rwork0.19979 ---
all0.202 141630 --
obs0.20227 117587 87.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.119 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20.9 Å21.82 Å2
2---0.08 Å20.85 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9648 0 425 876 10949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONr_bond_refined_d0.01810325
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.56414004
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.551211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1171505
X-RAY DIFFRACTIONr_gen_planes_refined0.0097860
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.235103
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.166635
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.25958
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.19416
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0216095
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8619767
X-RAY DIFFRACTIONr_scbond_it3.0494230
X-RAY DIFFRACTIONr_scangle_it4.8664237
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 224
Rwork0.309 4256

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