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- PDB-1hmo: THE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION -

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Entry
Database: PDB / ID: 1hmo
TitleTHE STRUCTURE OF DEOXY AND OXY HEMERYTHRIN AT 2.0 ANGSTROMS RESOLUTION
ComponentsHEMERYTHRIN
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


oxygen carrier activity / iron ion binding
Similarity search - Function
Haemerythrin / Hemerythrin-like / Hemerythrin, metal-binding domain / Haemerythrin, iron-binding site / Hemerythrin-like superfamily / : / Hemerythrin family signature. / Hemerythrin-like / Hemerythrin HHE cation binding domain / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Haemerythrin / Hemerythrin-like / Hemerythrin, metal-binding domain / Haemerythrin, iron-binding site / Hemerythrin-like superfamily / : / Hemerythrin family signature. / Hemerythrin-like / Hemerythrin HHE cation binding domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETYL GROUP / MU-OXO-DIIRON / OXYGEN MOLECULE / Hemerythrin
Similarity search - Component
Biological speciesThemiste dyscritum (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHolmes, M.A. / Letrong, I. / Turley, S. / Sieker, L.C. / Stenkamp, R.E.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Structures of deoxy and oxy hemerythrin at 2.0 A resolution.
Authors: Holmes, M.A. / Le Trong, I. / Turley, S. / Sieker, L.C. / Stenkamp, R.E.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: Active Site Structures of Deoxyhemerythrin and Oxyhemerythrin
Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. / Mccallum, J.D. / Sanders-Loehr, J.
#2: Journal: J.Am.Chem.Soc. / Year: 1984
Title: Binuclear Iron Complexes in Methemerythrin and Azidomethemerythrin at 2.0-Angstroms Resolution
Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1983
Title: Adjustment of Restraints in the Refinement of Methemerythrin and Azidomethemerythrin at 2.0 Angstroms Resolution.
Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1982
Title: Restrained Least-Squares Refinement of Themiste Dyscritum Methydroxohemerythrin at 2.0 Angstroms Resolution
Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H.
#5: Journal: Nature / Year: 1981
Title: Structure of the Binuclear Iron Complex in Metazidohaemerythrin from Themiste Dyscritum at 2.2 Angstroms Resolution
Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. / Sanders-Loehr, J.
#6: Journal: J.Biol.Chem. / Year: 1978
Title: Amino Acid Sequence of Hemerythrin from Themiste Dyscritum.
Authors: Stenkamp, R.E. / Lammers, P.J. / Brimhall, B. / Hermodson, M.A.
#7: Journal: J.Mol.Biol. / Year: 1978
Title: Crystallographic Studies of Azide, Thiocyanate and Perchlorate Complexes of Methemerythrin
Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H.
#8: Journal: Biochemistry / Year: 1978
Title: Structure of Methemerythrin at 2.8-Angstroms Resolution. Computer Graphics Fit of an Averaged Electron Density Map
Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. / Mcqueenjunior, J.E.
#9: Journal: J.Mol.Biol. / Year: 1976
Title: Structure of Methemerythrin at 5 Angstroms Resolution
Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H. / Loehr, J.S.
#10: Journal: Proc.Natl.Acad.Sci.USA / Year: 1976
Title: Structure of the Iron Complex in Methemerythrin
Authors: Stenkamp, R.E. / Sieker, L.C. / Jensen, L.H.
#11: Journal: J.Mol.Biol. / Year: 1975
Title: An X-Ray Crystallographic Study of Hemerythrin
Authors: Loehr, J.S. / Meyerhoff, K.N. / Sieker, L.C. / Jensen, L.H.
History
DepositionOct 18, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 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.ptnr2_label_atom_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.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,29116
Polymers53,4764
Non-polymers81512
Water5,080282
1
A: HEMERYTHRIN
B: HEMERYTHRIN
hetero molecules

A: HEMERYTHRIN
B: HEMERYTHRIN
hetero molecules

A: HEMERYTHRIN
B: HEMERYTHRIN
hetero molecules

A: HEMERYTHRIN
B: HEMERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,58232
Polymers106,9528
Non-polymers1,63024
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area17930 Å2
ΔGint-199 kcal/mol
Surface area35350 Å2
MethodPISA, PQS
2
C: HEMERYTHRIN
D: HEMERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1458
Polymers26,7382
Non-polymers4076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17830 Å2
ΔGint-208 kcal/mol
Surface area35490 Å2
MethodPISA
3
C: HEMERYTHRIN
D: HEMERYTHRIN
hetero molecules

C: HEMERYTHRIN
D: HEMERYTHRIN
hetero molecules

C: HEMERYTHRIN
D: HEMERYTHRIN
hetero molecules

C: HEMERYTHRIN
D: HEMERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,58232
Polymers106,9528
Non-polymers1,63024
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.690, 86.690, 80.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Atom site foot note1: HYDROGEN BONDING WOULD ARGUE FOR INTERCHANGING THE SIDECHAIN N AND O ATOMS OF ASN 40 AND GLN 59.
2: SERINE 64 IS ACETYLATED. / 3: PRO 7 OF EACH CHAIN IS A CIS PROLINE.

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Components

#1: Protein
HEMERYTHRIN


Mass: 13368.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Themiste dyscritum (invertebrata) / References: UniProt: P02246
#2: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O
#3: Chemical
ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2O
#4: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE BINUCLEAR IRON COMPLEX (DESIGNATED FEO BELOW) CONSISTS OF TWO FE ATOMS BRIDGED BY A MU-OXYGEN ...THE BINUCLEAR IRON COMPLEX (DESIGNATED FEO BELOW) CONSISTS OF TWO FE ATOMS BRIDGED BY A MU-OXYGEN ATOM, POSSIBLY A HYDROXIDE. FE1 IS HEXACOORDINATE AND FE2 IS PENTACOORDINATE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.1 mMprotein1buttom
20.08 MTris-HCl1reservior
30.02 MTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Observed criterion σ(F): 2 / Rmerge F obs: 0.029

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2→10 Å /
RfactorNum. reflection
obs0.173 40413
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 32 282 4098
Refinement
*PLUS
Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_plane_restr0.02

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