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Basic information

Entry
Database: PDB / ID: 4yd9
TitleCrystal structure of squid hemocyanin
Components(hemocyanin) x 3
KeywordsOXYGEN TRANSPORT / decamer / supermolecule
Function / homologyCU2-O2 CLUSTER
Function and homology information
Biological speciesTodarodes pacificus (Japanese flying squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMatsuno, A. / Gai, Z. / Kato, K. / Tanaka, Y. / Yao, M.
CitationJournal: Structure / Year: 2015
Title: Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 angstrom Resolution
Authors: Gai, Z. / Matsuno, A. / Kato, K. / Kato, S. / Khan, M.R.I. / Shimizu, T. / Yoshioka, T. / Kato, Y. / Kishimura, H. / Kanno, G. / Miyabe, Y. / Terada, T. / Tanaka, Y. / Yao, M.
History
DepositionFeb 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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
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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hemocyanin
B: hemocyanin
C: hemocyanin
D: hemocyanin
E: hemocyanin
F: hemocyanin
G: hemocyanin
H: hemocyanin
I: hemocyanin
J: hemocyanin
K: hemocyanin
L: hemocyanin
M: hemocyanin
N: hemocyanin
O: hemocyanin
P: hemocyanin
Q: hemocyanin
R: hemocyanin
S: hemocyanin
T: hemocyanin
U: hemocyanin
V: hemocyanin
W: hemocyanin
X: hemocyanin
Y: hemocyanin
Z: hemocyanin
a: hemocyanin
b: hemocyanin
c: hemocyanin
d: hemocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,835,836160
Polymers3,797,02430
Non-polymers38,812130
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170720 Å2
ΔGint-1440 kcal/mol
Surface area1087470 Å2
Unit cell
Length a, b, c (Å)171.370, 538.660, 310.920
Angle α, β, γ (deg.)90.00, 104.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 30 molecules ADGJMPSVYbBEHKNQTWZcCFILORUXad

#1: Protein
hemocyanin


Mass: 228841.391 Da / Num. of mol.: 10 / Fragment: N-terminal residues 1-2000 / Source method: isolated from a natural source
Source: (natural) Todarodes pacificus (Japanese flying squid)
#2: Protein
hemocyanin


Mass: 105798.141 Da / Num. of mol.: 10 / Fragment: residues 2001-2920 / Source method: isolated from a natural source
Source: (natural) Todarodes pacificus (Japanese flying squid)
#3: Protein
hemocyanin


Mass: 45062.883 Da / Num. of mol.: 10 / Fragment: C-terminal residues 2921-3314 / Source method: isolated from a natural source
Source: (natural) Todarodes pacificus (Japanese flying squid)

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Sugars , 5 types, 50 molecules

#4: 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.: 29
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
#5: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 1 types, 80 molecules

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


Mass: 159.091 Da / Num. of mol.: 80 / Source method: obtained synthetically / Formula: Cu2O2

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Details

Sequence detailsTHREE ENTITIES IN THIS STRUCTURE ARE FRAGMENTS OF THE ENTIRE PROTEIN. HOWEVER, THE TRACE AMONG ...THREE ENTITIES IN THIS STRUCTURE ARE FRAGMENTS OF THE ENTIRE PROTEIN. HOWEVER, THE TRACE AMONG FRAGMENTS WERE NOT IDENTIFIED CERTAINLY, SO THAT THE FRAGMENTS WERE ASSIGNED DIFFERENT CHAIN IDS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, HEPES, CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→49.1 Å / Num. obs: 1072359 / % possible obs: 98.9 % / Redundancy: 2.56 % / Rsym value: 0.113 / Net I/σ(I): 7.76

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3j32

3j32


Resolution: 3→49.099 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3031 53586 5 %
Rwork0.2739 --
obs0.2753 1072313 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms229780 0 2050 0 231830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011269507
X-RAY DIFFRACTIONf_angle_d1.402365491
X-RAY DIFFRACTIONf_dihedral_angle_d18.41598170
X-RAY DIFFRACTIONf_chiral_restr0.07638557
X-RAY DIFFRACTIONf_plane_restr0.00947390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9999-3.0340.412618000.377133855X-RAY DIFFRACTION99
3.034-3.06970.39917750.362234145X-RAY DIFFRACTION99
3.0697-3.10710.380217970.352834083X-RAY DIFFRACTION99
3.1071-3.14640.392617970.352233969X-RAY DIFFRACTION99
3.1464-3.18780.38617770.347334091X-RAY DIFFRACTION99
3.1878-3.23150.382618480.342134100X-RAY DIFFRACTION99
3.2315-3.27760.376417190.333934080X-RAY DIFFRACTION99
3.2776-3.32650.361418160.327434107X-RAY DIFFRACTION99
3.3265-3.37850.352718100.317334076X-RAY DIFFRACTION99
3.3785-3.43390.365417530.315734065X-RAY DIFFRACTION99
3.4339-3.49310.341118080.305433902X-RAY DIFFRACTION99
3.4931-3.55660.34517910.298534007X-RAY DIFFRACTION99
3.5566-3.6250.327817910.297234016X-RAY DIFFRACTION99
3.625-3.69890.333317860.291233948X-RAY DIFFRACTION99
3.6989-3.77930.31517870.277133964X-RAY DIFFRACTION99
3.7793-3.86720.311818030.277734015X-RAY DIFFRACTION99
3.8672-3.96390.289617730.265333806X-RAY DIFFRACTION99
3.9639-4.0710.302617840.272234038X-RAY DIFFRACTION99
4.071-4.19070.294217970.262833990X-RAY DIFFRACTION99
4.1907-4.32590.281917680.254933891X-RAY DIFFRACTION99
4.3259-4.48040.269317810.241333906X-RAY DIFFRACTION99
4.4804-4.65970.25717900.235933875X-RAY DIFFRACTION99
4.6597-4.87160.266617880.238933958X-RAY DIFFRACTION99
4.8716-5.12820.260717830.239733806X-RAY DIFFRACTION99
5.1282-5.44910.269417870.24133921X-RAY DIFFRACTION99
5.4491-5.86920.285117640.255133866X-RAY DIFFRACTION98
5.8692-6.45860.281517870.255333827X-RAY DIFFRACTION98
6.4586-7.39050.281617740.263133909X-RAY DIFFRACTION98
7.3905-9.30090.26117880.23833916X-RAY DIFFRACTION98
9.3009-49.1060.280517640.263633595X-RAY DIFFRACTION97

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