[English] 日本語
Yorodumi
- PDB-2vhb: AZIDE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA STERCORARIA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vhb
TitleAZIDE ADDUCT OF THE BACTERIAL 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
AZIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Bacterial hemoglobin
Similarity search - Component
Biological speciesVitreoscilla stercoraria (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.76 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 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEMOGLOBIN
B: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8986
Polymers31,5812
Non-polymers1,3174
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.720, 40.190, 62.940
Angle α, β, γ (deg.)90.00, 106.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.24016, -0.00448, -0.97072), (-0.01317, -0.99991, 0.00136), (-0.97064, 0.01246, -0.2402)
Vector: 68.70651, 20.92279, 89.09117)

-
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-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 52 %
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. AZIDE SOAKING ...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. AZIDE SOAKING CONDITIONS: 0.03 M N3-, 1 HOUR, PH 7.0, 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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1
DetectorType: MAR RESEARCH 180MM IMAGE PLATE / Detector: IMAGE PLATE AREA DETECTOR / Date: Oct 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→15 Å / Num. obs: 29076 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 22
Reflection shellResolution: 1.76→1.83 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 2 / Rsym value: 0.049 / % possible all: 94.1
Reflection
*PLUS
Num. measured all: 68840

-
Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 1.76→15 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.197 --
obs-29629 92 %
Refinement stepCycle: LAST / Resolution: 1.76→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 92 184 2353
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.013221124
X-RAY DIFFRACTIONt_angle_deg1.987299713
X-RAY DIFFRACTIONt_dihedral_angle_d14.254125515
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0195320
X-RAY DIFFRACTIONt_gen_planes0.0230650
X-RAY DIFFRACTIONt_it4.932210718
X-RAY DIFFRACTIONt_nbd0.054105100
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg14.25415
X-RAY DIFFRACTIONt_planar_d0.01920
X-RAY DIFFRACTIONt_plane_restr0.0250

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more