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- PDB-3vhb: IMIDAZOLE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA SP. -

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Basic information

Entry
Database: PDB / ID: 3vhb
TitleIMIDAZOLE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA SP.
ComponentsPROTEIN (HEMOGLOBIN)
KeywordsOXYGEN STORAGE/TRANSPORT / HEMOPROTEIN / OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitric oxide dioxygenase NAD(P)H activity / cellular response to nitrosative stress / nitric oxide catabolic process / FAD binding / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Bacterial hemoglobin
Similarity search - Component
Biological speciesVitreoscilla stercoraria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsBolognesi, M. / Boffi, A. / Coletta, M. / Mozzarelli, A. / Pesce, A. / Tarricone, C. / Ascenzi, P.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Anticooperative ligand binding properties of recombinant ferric Vitreoscilla homodimeric hemoglobin: a thermodynamic, kinetic and X-ray crystallographic study.
Authors: Bolognesi, M. / Boffi, A. / Coletta, M. / Mozzarelli, A. / Pesce, A. / Tarricone, C. / Ascenzi, P.
History
DepositionMar 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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: PROTEIN (HEMOGLOBIN)
B: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9526
Polymers31,5812
Non-polymers1,3714
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.640, 41.730, 61.560
Angle α, β, γ (deg.)90.00, 105.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (-1), (1), (-1) / Vector: 20.09485)

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Components

#1: Protein 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 / 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: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 52 %
Crystal growpH: 6.4
Details: AMMONIUM SULFATE 1.3M, 0.1 M PYROPHOSPHATE, 3% ETHYLENE GLYCOLE, PH 6.4. IMIDAZOLE SOAKING CONDITION: 0.05M IMIDAZOLE FOR 30 MIN.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4.0 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 Mammonium sulfate1reservoir
20.10 Mpyrophosphate1reservoir
33 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 5335 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rsym value: 0.07 / Net I/σ(I): 17
Reflection
*PLUS
Num. measured all: 17072 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
CCP4model building
TNT5Erefinement
MOSFLMdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.1→15 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.238 17072 -
obs-17072 100 %
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 96 87 2225
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.015219035
X-RAY DIFFRACTIONt_angle_deg2.568296460
X-RAY DIFFRACTIONt_dihedral_angle_d17.76712420
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0115440
X-RAY DIFFRACTIONt_gen_planes0.018313140
X-RAY DIFFRACTIONt_it5.357208865
X-RAY DIFFRACTIONt_nbd0.06276240
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / σ(F): 0 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d35
X-RAY DIFFRACTIONt_angle_deg60
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg017.767
X-RAY DIFFRACTIONt_planar_d400.011
X-RAY DIFFRACTIONt_plane_restr1400.018

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