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- PDB-1hr3: STRUCTURE OF TRIMERIC HAEMERYTHRIN -

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Basic information

Entry
Database: PDB / ID: 1hr3
TitleSTRUCTURE OF TRIMERIC HAEMERYTHRIN
ComponentsHEMERYTHRIN
KeywordsOXYGEN TRANSPORT PROTEIN
Function / homologyMONOAZIDO-MU-OXO-DIIRON
Function and homology information
Biological speciesSiphonosoma (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 5.5 Å
AuthorsSmith, J.L. / Hendrickson, W.A. / Addison, A.W.
Citation
Journal: Nature / Year: 1983
Title: Structure of trimeric haemerythrin.
Authors: Smith, J.L. / Hendrickson, W.A. / Addison, A.W.
#1: Journal: Arch.Biochem.Biophys. / Year: 1977
Title: Chemistry of Phascolosoma Lurco Hemerythrin
Authors: Addison, A.W. / Bruce, R.E.
History
DepositionMay 6, 1983Processing site: BNL
Revision 1.0Jun 10, 1983Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,6906
Polymers30,1813
Non-polymers5093
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.310, 45.110, 63.580
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES 7 AND 90 ARE CIS-PROLINES
2: FEA IS MONOAZIDO-MU-OXO-DIIRON. ONLY THE COORDINATES FOR THE TWO IRON ATOMS ARE PRESENT IN THIS ENTRY. SEE REMARK 7.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.03309, 0.59094, -0.80604), (0.78532, 0.51422, 0.34473), (0.61821, -0.62159, -0.48109)15.42, -4.91, 40.7
2given(-0.03309, 0.78532, 0.61821), (0.59094, 0.51422, -0.62159), (-0.80604, 0.34476, -0.48109)-20.79, 18.71, 33.7
DetailsAPPLYING THE TRANSFORMATION GIVEN ON THE MTRIX 1 RECORDS BELOW TO SUBUNIT 1 (CHAIN IDENTIFIER A) WILL YIELD APPROXIMATE COORDINATES FOR SUBUNIT 2 (CHAIN IDENTIFIER B). FOR THIS TRANSFORMATION PHI=11.37, PSI=34.69, CHI=120.00, WHERE PHI, PSI, CHI FOLLOW THE CONVENTION OF M.G.ROSSMANN AND D.M.BLOW (ACTA CRYSTALLOGR., V. 15, P. 24 (1962)). APPLYING THE TRANSFORMATION GIVEN ON THE MTRIX 2 RECORDS BELOW TO SUBUNIT 1 (CHAIN IDENTIFIER A) WILL YIELD APPROXIMATE COORDINATES FOR SUBUNIT 3 (CHAIN IDENTIFIER C). FOR THIS TRANSFORMATION PHI=11.37, PSI=34.69, CHI=-120.00.

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Components

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


Mass: 10060.393 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siphonosoma (invertebrata)
#2: Chemical ChemComp-FEA / MONOAZIDO-MU-OXO-DIIRON


Mass: 169.709 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2N3O
Nonpolymer detailsBECAUSE THIS IS A CA COORDINATE SET, THE CONNECTIVITY OF THE IRON ATOMS OF FEA CANNOT BE SPECIFIED ...BECAUSE THIS IS A CA COORDINATE SET, THE CONNECTIVITY OF THE IRON ATOMS OF FEA CANNOT BE SPECIFIED ON CONECT RECORDS. THE CONNECTIVITY IS AS FOLLOWS FE1 NE2 HIS 73 NE2 HIS 77 NE2 HIS 106 OE1 GLU 58 OD1 ASP 111 0 FEA 1 FE2 NE2 HIS 25 NE2 HIS 54 OE2 GLU 58 OD2 ASP 111 O FEA 1 N1 FEA 1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.66 %
Crystal grow
*PLUS
Method: vapor diffusion / Details: referred to J.Biol.Chem. 257.9883-9886 1982
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5-5.0 mg/mlprotein1drop
2cacodylate1drop
3PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS

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Processing

RefinementHighest resolution: 5.5 Å
Refinement stepCycle: LAST / Highest resolution: 5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms354 0 6 0 360
Refinement
*PLUS
Highest resolution: 5.5 Å / Rfactor obs: 0.336
Solvent computation
*PLUS
Displacement parameters
*PLUS

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