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- PDB-1hrb: ATOMIC MODELS FOR THE POLYPEPTIDE BACKBONES OF MYOHEMERYTHRIN AND... -

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Basic information

Entry
Database: PDB / ID: 1hrb
TitleATOMIC MODELS FOR THE POLYPEPTIDE BACKBONES OF MYOHEMERYTHRIN AND HEMERYTHRIN
ComponentsHEMERYTHRIN B
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


oxygen carrier activity / iron ion binding
Similarity search - Function
Haemerythrin / Hemerythrin, metal-binding domain / Haemerythrin, iron-binding site / Hemerythrin-like superfamily / : / Hemerythrin family signature. / Hemerythrin-like / Hemerythrin HHE cation binding domain
Similarity search - Domain/homology
Biological speciesPhascolopsis gouldii (peanut worm)
MethodX-RAY DIFFRACTION / Resolution: 5.5 Å
AuthorsHendrickson, W.A. / Ward, K.B.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 1975
Title: Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin.
Authors: Hendrickson, W.A. / Ward, K.B.
#1: Journal: Nature / Year: 1975
Title: Quaternary and Tertiary Structure of Haemerythrin
Authors: Ward, K.B. / Hendrickson, W.A. / Klippenstein, G.L.
#2: Journal: Science / Year: 1976
Title: Hemerythrin. Alternative Oxygen Carrier
Authors: Klotz, I.M. / Klippenstein, G.L. / Hendrickson, W.A.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975
Title: Tertiary Structure of Myohemerythrin at Low Resolution
Authors: Hendrickson, W.A. / Klippenstein, G.L. / Ward, K.B.
#4: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
History
DepositionJun 23, 1976Processing site: BNL
Revision 1.0Sep 28, 1978Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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 / 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 / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: HEMERYTHRIN B
B: HEMERYTHRIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0196
Polymers26,7962
Non-polymers2234
Water00
1
A: HEMERYTHRIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5103
Polymers13,3981
Non-polymers1122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HEMERYTHRIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5103
Polymers13,3981
Non-polymers1122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.820, 104.820, 54.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (0.707107, 0.707107), (-0.707107, 0.707107), (1) / Vector: 74.118933, 27.04)

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Components

#1: Protein HEMERYTHRIN B / Coordinate model: Cα atoms only


Mass: 13398.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phascolopsis gouldii (peanut worm) / Tissue: COELOMIC FLUID / References: UniProt: P02244
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 5.5 Å
Refinement stepCycle: LAST / Highest resolution: 5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms226 0 4 0 230

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