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- PDB-2hmq: THE STRUCTURES OF MET AND AZIDOMET HEMERYTHRIN AT 1.66 ANGSTROMS ... -

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Entry
Database: PDB / ID: 2hmq
TitleTHE STRUCTURES OF MET AND AZIDOMET HEMERYTHRIN AT 1.66 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
ACETATE ION / MU-OXO-DIIRON / Hemerythrin
Similarity search - Component
Biological speciesThemiste dyscritum (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 1.66 Å
AuthorsHolmes, M.A. / Stenkamp, R.E.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Structures of met and azidomet hemerythrin at 1.66 A resolution.
Authors: Holmes, M.A. / 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, L.
#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.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.
#7: 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.
#8: Journal: J.Biol.Chem. / Year: 1978
Title: Amino Acid Sequence of Hemerythrin from Themiste Dyscritum
Authors: Loehr, J.S. / Lammers, P.J. / Brimhall, B. / Hermodson, M.A.
#9: 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.
#10: 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.
#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
SupersessionJan 15, 1992ID: 1HMQ
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,15912
Polymers53,4124
Non-polymers7478
Water5,278293
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)108,31824
Polymers106,8248
Non-polymers1,49416
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 area17000 Å2
ΔGint-208 kcal/mol
Surface area35210 Å2
MethodPISA, PQS
2
C: HEMERYTHRIN
D: HEMERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0796
Polymers26,7062
Non-polymers3734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17040 Å2
ΔGint-209 kcal/mol
Surface area35180 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)108,31824
Polymers106,8248
Non-polymers1,49416
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)86.600, 86.600, 80.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Atom site foot note1: PRO 7 IS A CIS-PROLINE.
2: VAL 21 IS MODELED AS VAL AND ILE EACH WITH HALF OCCUPANCY.
3: ALA 64 IS MODELED AS AN ACETYLATED SERINE.
4: THE SIDE CHAINS OF THE FOLLOWING RESIDUES ARE DISORDERED: CHAIN A - 28, 53, 72, 81, 100, 108 CHAIN B - 72, 100 CHAIN D - 100
5: HYDROGEN BONDING WOULD ARGUE FOR INTERCHANGING THE SIDE-CHAIN N AND O ATOMS FOR RESIDUES ASN 40 AND GLU 59.

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Components

#1: Protein
HEMERYTHRIN


Mass: 13352.996 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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. FE1 IS HEXA-COORDINATE AND FE2 IS PENTA-COORDINATE.
Sequence detailsRESIDUE 21 HAS BEEN MODELED BOTH AS VAL AND AS ILE. IT IS PRESENTED IN THE ATOM RECORDS BELOW AS ...RESIDUE 21 HAS BEEN MODELED BOTH AS VAL AND AS ILE. IT IS PRESENTED IN THE ATOM RECORDS BELOW AS ILE 21A FOLLOWED BY VAL 21B. ALL ATOMS OF THIS RESIDUE HAVE BEEN ASSIGNED OCCUPANCIES OF 0.5.

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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: 56.67 %
Crystal grow
*PLUS
Method: microdialysis
Details: referred to 'Loehr, J.S.', (1975) J.Mol.Biol., 91, 521-525
Components of the solutions
*PLUS
Conc.: 35 % / Common name: MPD

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.66→10 Å
Details: THE SIDE CHAINS OF THE FOLLOWING RESIDUES ARE DISORDERED: CHAIN A - 28, 53, 72, 81, 100, 108 CHAIN B - 72, 100 CHAIN D - 100
RfactorNum. reflection
obs0.189 65683
Refinement stepCycle: LAST / Resolution: 1.66→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 28 293 4129
Refinement
*PLUS
Highest resolution: 1.66 Å / Lowest resolution: 10 Å / Rfactor obs: 0.189 / Num. reflection obs: 65683
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.023
X-RAY DIFFRACTIONo_plane_restr0.023

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