[English] 日本語
Yorodumi
- PDB-1hds: MACROMOLECULAR STRUCTURE REFINEMENT BY RESTRAINED LEAST-SQUARES A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hds
TitleMACROMOLECULAR STRUCTURE REFINEMENT BY RESTRAINED LEAST-SQUARES AND INTERACTIVE GRAPHICS AS APPLIED TO SICKLING DEER TYPE III HEMOGLOBIN
Components
  • HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
  • HEMOGLOBIN S (DEOXY) (BETA CHAIN)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle ...haptoglobin binding / organic acid binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily ...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-1/2 / Hemoglobin subunit beta-3
Similarity search - Component
Biological speciesOdocoileus virginianus (white-tailed deer)
MethodX-RAY DIFFRACTION / Resolution: 1.98 Å
AuthorsAmma, E.L. / Girling, R.L.
Citation
Journal: Acta Crystallogr.,Sect.A / Year: 1980
Title: Macromolecular Structure Refinement by Restrained Least-Squares and Interactive Graphics as Applied to Sickling Deer Type III Hemoglobin
Authors: Girling, R.L. / Houston, T.E. / Schmidtjunior, W.C. / Amma, E.L.
#1: Journal: J.Mol.Biol. / Year: 1979
Title: Molecular packing and intermolecular contacts of sickling deer type III hemoglobin.
Authors: Girling, R.L. / Schmidt Jr., W.C. / Houston, T.E. / Amma, E.L. / Huisman, T.H.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1977
Title: Application of a Restrained Least-Squares Refinement Procedure to Sickling Deer Hemoglobin
Authors: Schmidtjunior, W.C. / Girling, R.L. / Amma, E.L.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1977
Title: The Structure of Sickling Deer Type III Hemoglobin by Molecular Replacement
Authors: Schmidtjunior, W.C. / Girling, R.L. / Houston, T.E. / Sproul, G.D. / Amma, E.L. / Huisman, T.H.J.
#4: Journal: Atlas of Protein Sequence and Structure,Supplement 3
Year: 1978
Authors: Dayhoff, M.O.
History
DepositionOct 1, 1979Processing site: BNL
Revision 1.0Dec 7, 1979Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2020Group: Data collection / Database references / Other
Category: citation / citation_author ...citation / citation_author / citation_editor / pdbx_database_status / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
B: HEMOGLOBIN S (DEOXY) (BETA CHAIN)
C: HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
D: HEMOGLOBIN S (DEOXY) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4598
Polymers61,9934
Non-polymers2,4664
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.500, 70.830, 65.950
Angle α, β, γ (deg.)90.00, 94.15, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: THE CHIRALITY OF THIS RESIDUE APPEARS TO BE IN ERROR AND WILL BE CORRECTED IN SUBSEQUENT REFINEMENT CYCLES.

-
Components

#1: Protein HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)


Mass: 15215.339 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Odocoileus virginianus (white-tailed deer)
References: UniProt: P01972
#2: Protein HEMOGLOBIN S (DEOXY) (BETA CHAIN)


Mass: 15781.243 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Odocoileus virginianus (white-tailed deer)
References: UniProt: P02074
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal grow
*PLUS
pH: 6.3 / Method: microdialysis
Details: Schmidtjunior, W.C., (1977) Acta Crystallogr.,Sect.B, 33, 335.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.6 Mphosphate11
30.25-0.45 Mammonium sulfate12
42.85 Mmonobasic sodium12
52.90 Mdibasic potassium phosphates12
2Hb(DIII)113.0g%

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

RefinementHighest resolution: 1.98 Å
Details: TO DERIVE THE COORDINATES BASED ON THE ORTHOGONAL ANGSTROM SYSTEM STANDARD FOR HEMOGLOBINS THE FOLLOWING TRANSFORMATION MUST BE APPLIED TO THE COORDINATES GIVEN BELOW. FIRST, FORM THE ...Details: TO DERIVE THE COORDINATES BASED ON THE ORTHOGONAL ANGSTROM SYSTEM STANDARD FOR HEMOGLOBINS THE FOLLOWING TRANSFORMATION MUST BE APPLIED TO THE COORDINATES GIVEN BELOW. FIRST, FORM THE TRANSLATED VECTOR FROM X, Y, Z BY XT = X - 26.3830 YT = Y - .2020 ZT = Z - 11.3585 THEN APPLY THE FOLLOWING MATRIX TO THE VECTOR XT, YT, ZT. .4216 .3898 .8187 -.7645 -.3414 .5433 .5150 -.8387 .1771 IN THIS TRANSFORMED SYSTEM THE Y AXIS IS THE MOLECULAR DIAD RELATING ALPHA-1 TO ALPHA-2 AND THE X AXIS IS THE PSEUDO DIAD WHICH RELATES ALPHA-1 TO BETA-1.
Refinement stepCycle: LAST / Highest resolution: 1.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 172 0 4556

+
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