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- PDB-1hds: MACROMOLECULAR STRUCTURE REFINEMENT BY RESTRAINED LEAST-SQUARES A... -

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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


hemoglobin complex / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, alpha-type / Hemoglobin, beta-type / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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%

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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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

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