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- PDB-1js8: Structure of a Functional Unit from Octopus Hemocyanin -

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Basic information

Entry
Database: PDB / ID: 1js8
TitleStructure of a Functional Unit from Octopus Hemocyanin
ComponentsHemocyanin
KeywordsOXYGEN STORAGE/TRANSPORT / GLYCOPROTEIN / MOLLUSC / OXYGEN-TRANSPORT / THIOETHER BOND / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


oxygen carrier activity / oxidoreductase activity / metal ion binding
Similarity search - Function
Haemocyanin C-terminal domain / Hemocyanin; Chain: A, domain 2 / Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Haemocyanin beta-sandwich / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. ...Haemocyanin C-terminal domain / Hemocyanin; Chain: A, domain 2 / Haemocyanin beta-sandwich domain / Haemocyanin C-terminal domain superfamily / Haemocyanin beta-sandwich / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CU2-O2 CLUSTER / alpha-D-mannopyranose / Hemocyanin G-type, units Oda to Odg
Similarity search - Component
Biological speciesOctopus dofleini (giant octopus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS, combined with partial MAD phasing / Resolution: 2.3 Å
AuthorsCuff, M.E. / Miller, K.I. / van Holde, K.E. / Hendrickson, W.A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of a functional unit from Octopus hemocyanin.
Authors: Cuff, M.E. / Miller, K.I. / van Holde, K.E. / Hendrickson, W.A.
History
DepositionAug 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The native whole molecule cannot be generated from this information alone. Octopus hemocyanin is a 3.5MDa protein composed of 10 polypeptide subunits arranged about a D5 molecular symmetry axis. Each 350 kDa subunit contains 7 similar oxygen-binding functional units which occur serially along the polypeptide. Odg (this deposition) contains the C-terminal functional unit.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemocyanin
B: Hemocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2828
Polymers89,6202
Non-polymers2,6626
Water5,332296
1
A: Hemocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3844
Polymers44,8101
Non-polymers1,5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8984
Polymers44,8101
Non-polymers1,0883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.860, 168.390, 58.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hemocyanin / / HEMOCYANIN G-TYPE


Mass: 44810.062 Da / Num. of mol.: 2 / Fragment: C-terminal functional unit, Odg / Source method: isolated from a natural source
Details: C-TERMINAL PROTEOLYTIC FRAGMENT FROM 350KDA POLYPEPTIDE SUBUNIT. NATIVE MULTIMER IS 10 SUBUNITS EXHIBITING D5 SYMMETRY.
Source: (natural) Octopus dofleini (giant octopus) / Strain: G-type sequence / References: UniProt: O61363

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Sugars , 4 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpb1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-3-4-4-4/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpb1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 298 molecules

#6: Chemical ChemComp-CUO / CU2-O2 CLUSTER / CU-O2-CU LINKAGE


Mass: 159.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe refinement statistics suggest that this well-ordered region contains a LEU.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 15

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, LITHIUM SULFATE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: Cuff, M.E., (1990) J. Mol. Biol., 213, 11.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12791
22981
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory PHOTON FACTORY BEAMLINE11.3796,1.3779,1.2000
SYNCHROTRONNSLS X4A20.98
Detector
TypeIDDetectorDate
FUJI1IMAGE PLATEJun 1, 1989
FUJI2IMAGE PLATEJun 1, 1994
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1SAGITALLY FOCUSED Si(111)
Radiation wavelength
IDWavelength (Å)Relative weight
11.37961
21.37791
31.21
40.981
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 94.8 % / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATAdata reduction
MADSYSphasing
MLPHAREphasing
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MIRAS, combined with partial MAD phasing
Resolution: 2.3→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 1614 RANDOM
Rwork0.202 --
obs0.201 38644 -
all-39114 -
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6134 0 163 296 6593
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_d1.69
X-RAY DIFFRACTIONx_dihedral_angle_d24.29
X-RAY DIFFRACTIONx_improper_angle_d1.443
X-RAY DIFFRACTIONx_mcbond_it0.09
Refine LS restraints NCSWeight Biso : 1 / Weight position: 50
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.3-2.380.2441490.214X-RAY DIFFRACTION2810
3.1-3.40.2442100.214X-RAY DIFFRACTION3723
4.79-100.2442080.214X-RAY DIFFRACTION3991
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.69
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.29
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.443
LS refinement shell
*PLUS
Rfactor Rfree: 0.244 / Rfactor Rwork: 0.214

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