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- PDB-1vhb: BACTERIAL DIMERIC HEMOGLOBIN FROM VITREOSCILLA STERCORARIA -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1vhb
TitleBACTERIAL DIMERIC HEMOGLOBIN FROM VITREOSCILLA STERCORARIA
ComponentsHEMOGLOBIN
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN
Function / homology
Function and homology information


cellular response to nitrosative stress / nitric oxide dioxygenase NAD(P)H activity / nitric oxide catabolic process / FAD binding / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bacterial hemoglobin
Similarity search - Component
Biological speciesVitreoscilla stercoraria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR-DENSITY MODIFICATION / Resolution: 1.83 Å
AuthorsTarricone, C. / Galizzi, A. / Coda, A. / Ascenzi, P. / Bolognesi, M.
CitationJournal: Structure / Year: 1997
Title: Unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from Vitreoscilla sp.
Authors: Tarricone, C. / Galizzi, A. / Coda, A. / Ascenzi, P. / Bolognesi, M.
History
DepositionFeb 19, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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_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 / _struct_conn.ptnr2_label_seq_id / _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: HEMOGLOBIN
B: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8144
Polymers31,5812
Non-polymers1,2332
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.320, 41.420, 62.940
Angle α, β, γ (deg.)90.00, 106.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (0.26808, -0.9634), (-1), (-0.9634, -0.26808) / Vector: 68.79999, 20.77, 90.56)

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Components

#1: Protein HEMOGLOBIN / SOLUBLE CYTOCHROME O


Mass: 15790.269 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitreoscilla stercoraria (bacteria) / Strain: C1 / Gene: VGB / Plasmid: PDH88 / Gene (production host): VGB / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P04252
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.3 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion / pH: 6.4
Details: PRECIPITANT: AMMONIUM SULFATE 1.2 M. BUFFER: PYROPHOSPHATE 0.2 M PH 6.4. ADDITIVES: ETHYLENE GLYCOL 3% V/V. PROTEIN CONCENTRATION 25 MG/ML. VAPOR DIFFUSION TECHNIQUES., vapor diffusion
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 Mammonium salfate11
20.1 Mpyrophosphate11
33 %(v/v)ethylene glycol11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW21B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→25 Å / Num. obs: 26582 / % possible obs: 94.9 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.36 / Net I/σ(I): 12.9
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / Rsym value: 0.36 / % possible all: 61
Reflection
*PLUS
Num. measured all: 101071

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Processing

Software
NameVersionClassification
SCALEITmodel building
SHELX90model building
MLPHAREphasing
SOLOMONphasing
DMmodel building
GLRFphasing
NCSMASKmodel building
TNT1refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
SCALEITphasing
SHELX-90phasing
DMphasing
NCSMASKphasing
RefinementMethod to determine structure: SIR-DENSITY MODIFICATION / Resolution: 1.83→15 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: A POSTERIORI / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1100 4.1 %EVERY 24TH REFLECTION
Rwork0.184 ---
all-27040 --
obs-27040 95 %-
Solvent computationBsol: 167 Å2 / ksol: 0.58 e/Å3
Refinement stepCycle: LAST / Resolution: 1.83→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 86 119 2247
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.011217824
X-RAY DIFFRACTIONt_angle_deg1.788295613
X-RAY DIFFRACTIONt_dihedral_angle_d13.148123615
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0155420
X-RAY DIFFRACTIONt_gen_planes0.01730250
X-RAY DIFFRACTIONt_it4.478207810
X-RAY DIFFRACTIONt_nbd0.043100
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.184 / Rfactor Rfree: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg13.14815
X-RAY DIFFRACTIONt_planar_d0.01520
X-RAY DIFFRACTIONt_plane_restr0.01750

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