[English] 日本語
Yorodumi
- PDB-2pgh: STRUCTURE DETERMINATION OF AQUOMET PORCINE HEMOGLOBIN AT 2.8 ANGS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pgh
TitleSTRUCTURE DETERMINATION OF AQUOMET PORCINE HEMOGLOBIN AT 2.8 ANGSTROM RESOLUTION
Components
  • HEMOGLOBIN (AQUO MET) (ALPHA CHAIN)
  • HEMOGLOBIN (AQUO MET) (BETA CHAIN)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / 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 / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsKatz, D.S. / White, S.P. / Huang, W. / Kumar, R. / Christianson, D.W.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Structure determination of aquomet porcine hemoglobin at 2.8 A resolution.
Authors: Katz, D.S. / White, S.P. / Huang, W. / Kumar, R. / Christianson, D.W.
#1: Journal: Cancer Detect.Prev. / Year: 1993
Title: Production of Hemoglobin in Transgenic Swine: An Approach to a Blood Substitute
Authors: O'Donnell, J.K. / Martin, M.J. / Logan, J.S. / Kumar, R.
#2: Journal: Biomater.,Artif.Cells, Immobilization Biotechnol. / Year: 1992
Title: The Purification and Comparative Analysis of Hemoglobin from Animal Bloods
Authors: Lee, C.J. / Kan, P. / Chen, W.K.
#3: Journal: Bio/Technology / Year: 1992
Title: Production of Functional Human Hemoglobin in Transgenic Swine
Authors: Swanson, M.E. / Martin, M.J. / O'Donnell, J.K. / Hoover, K. / Sago, W. / Huntress, V. / Parsons, C.T. / Pinkert, C.A. / Pilder, S. / Logan, J.S.
History
DepositionSep 16, 1994Processing site: BNL
SupersessionNov 30, 1994ID: 1PGH
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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_ref_seq_dif.details / _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 (AQUO MET) (ALPHA CHAIN)
B: HEMOGLOBIN (AQUO MET) (BETA CHAIN)
C: HEMOGLOBIN (AQUO MET) (ALPHA CHAIN)
D: HEMOGLOBIN (AQUO MET) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7138
Polymers62,2474
Non-polymers2,4664
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11270 Å2
ΔGint-108 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.600, 72.800, 115.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HEMOGLOBIN (AQUO MET) (ALPHA CHAIN)


Mass: 15064.144 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Tissue: BLOOD / Organ: BLOOD / References: UniProt: P01965
#2: Protein HEMOGLOBIN (AQUO MET) (BETA CHAIN)


Mass: 16059.345 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Tissue: BLOOD / Organ: BLOOD / References: UniProt: P02067
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE DEPOSITORS CONCLUDE THAT THEIR CRYSTALS ARE OF AQUOMET FORM BECAUSE: A) PRECAUTIONS SIMILAR TO ...THE DEPOSITORS CONCLUDE THAT THEIR CRYSTALS ARE OF AQUOMET FORM BECAUSE: A) PRECAUTIONS SIMILAR TO THOSE USED IN THE CRYSTALLIZATION OF HUMAN OXYHEMOGLOBIN (E.G., ADDITION OF CHELATING AGENTS OR BUBBLING OXYGEN INTO SOLUTIONS) WERE NOT USED. B) OXYHEMOGLOBIN AUTOOXIDIZES TO AQUOMET HEMOGLOBIN WITHOUT SUCH PRECAUTIONS. C) RE-DISSOLVED CRYSTALS EXHIBIT AN ABSORBANCE SPECTRUM CHARACTERISTIC OF THE AQUOMET FORM (MAXIMUM = 405 NM). HOWEVER, SOLVENT MOLECULES THAT COORDINATE TO EACH FE ATOM ARE NOT APPARENT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.5 mMpHb1dropsolubilized in 10 mM ammonium phosphate
22.8-2.9 M1reservoirNa+
32.8-2.9 M1reservoirK+

-
Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 13290 / Num. measured all: 44042 / Rmerge(I) obs: 0.087

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→6.5 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.154 -
obs0.154 13290
Refinement stepCycle: LAST / Resolution: 2.8→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 172 130 4700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.154 / Rfactor Rfree: 0.295
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.9
X-RAY DIFFRACTIONx_dihedral_angle_d21.3
X-RAY DIFFRACTIONx_dihedral_angle_deg2.3

+
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