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- PDB-1hcy: CRYSTAL STRUCTURE OF HEXAMERIC HAEMOCYANIN FROM PANULIRUS INTERRU... -

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Basic information

Entry
Database: PDB / ID: 1hcy
TitleCRYSTAL STRUCTURE OF HEXAMERIC HAEMOCYANIN FROM PANULIRUS INTERRUPTUS REFINED AT 3.2 ANGSTROMS RESOLUTION
ComponentsARTHROPODAN HEMOCYANIN
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


oxygen carrier activity / oxidoreductase activity / extracellular region / metal ion binding
Similarity search - Function
Hemocyanin, C-terminal domain / Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing domain ...Hemocyanin, C-terminal domain / Arthropod hemocyanins / insect LSPs signature 1. / Arthropod hemocyanins / insect LSPs signature 2. / Hemocyanin, N-terminal / Hemocyanin, N-terminal domain superfamily / Hemocyanin, all-alpha domain / Hemocyanin, C-terminal domain superfamily / Hemocyanin/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / Hemocyanin A chain
Similarity search - Component
Biological speciesPanulirus interruptus (California spiny lobster)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsVolbeda, A. / Hol, W.G.J.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Crystal structure of hexameric haemocyanin from Panulirus interruptus refined at 3.2 A resolution.
Authors: Volbeda, A. / Hol, W.G.
#1: Journal: Eur.J.Biochem. / Year: 1989
Title: Spectroscopic Investigations of Panulirus Interruptus Hemocyanin in the Crystalline State
Authors: Volbeda, A. / Feiters, M.C. / Vincent, M.G. / Bouwman, E. / Dobson, B. / Kalk, K.H. / Reedijk, J. / Hol, W.G.J.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Pseudo 2-Fold Symmetry in the Copper-Binding Domain of Arthropodan Haemocyanins. Possible Implications for the Evolution of Oxygen Transport Proteins
Authors: Volbeda, A. / Hol, W.G.J.
#3: Journal: Eur.J.Biochem. / Year: 1988
Title: Panulirus Interruptus Hemocyanin. The Amino Acid Sequence of Subunit B and Anomalous Behavior of Subunits a and B on Polyacrylamide Gel Electrophoresis in the Presence of /Sds
Authors: Jekel, P.A. / Bak, H.J. / Soeter, N.M. / Vereijken, J.M. / Beintema, J.J.
#4: Journal: Eur.J.Biochem. / Year: 1987
Title: Panulirus Interruptus Hemocyanin. The Elucidation of the Complete Amino Acid Sequence of Subunit A
Authors: Bak, H.J. / Beintema, J.J.
#5: Journal: J.Mol.Biol. / Year: 1986
Title: Structure Determination of Panulirus Interruptus Haemocyanin at 3.2 Angstroms Resolution. Successful Phase Extension by Sixfold Density Averaging
Authors: Gaykema, W.P.J. / Volbeda, A. / Hol, W.G.J.
#6: Journal: Science / Year: 1985
Title: The Structure of Arthropod Hemocyanins
Authors: Linzen, B. / Soeter, N.M. / Riggs, A.F. / Schneider, H.-J. / Schartau, W. / Moore, M.D. / Yokota, E. / Behrens, P.Q. / Nakashima, H. / Takagi, T. / Nemoto, T. / Vereijken, J.M. / Bak, H.J. / ...Authors: Linzen, B. / Soeter, N.M. / Riggs, A.F. / Schneider, H.-J. / Schartau, W. / Moore, M.D. / Yokota, E. / Behrens, P.Q. / Nakashima, H. / Takagi, T. / Nemoto, T. / Vereijken, J.M. / Bak, H.J. / Beintema, J.J. / Volbeda, A. / Gaykema, W.P.J. / Hol, W.G.J.
#7: Journal: Nature / Year: 1984
Title: 3.2 Angstroms Structure of the Copper-Containing, Oxygen-Carrying Protein Panulirus Interruptus Haemocyanin
Authors: Gaykema, W.P.J. / Hol, W.G.J. / Vereijken, J.M. / Soeter, N.M. / Bak, H.J. / Beintema, J.J.
History
DepositionMay 15, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARTHROPODAN HEMOCYANIN
B: ARTHROPODAN HEMOCYANIN
C: ARTHROPODAN HEMOCYANIN
D: ARTHROPODAN HEMOCYANIN
E: ARTHROPODAN HEMOCYANIN
F: ARTHROPODAN HEMOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)456,85114
Polymers454,1776
Non-polymers2,6738
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.800, 193.100, 122.200
Angle α, β, γ (deg.)90.00, 118.10, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUE PRO 625 IS A CIS PROLINE.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.994209, 0.092695, -0.05437), (0.092143, -0.995666, -0.012588), (-0.055301, 0.007505, -0.998442)1.39, 69.422, 165.741
2given(-0.509313, 0.029293, 0.860083), (-0.15271, 0.980483, -0.123823), (-0.846924, -0.194409, -0.494899)-72.001, 11.226, 131.92
3given(-0.476348, 0.140372, 0.867979), (0.108572, -0.970228, 0.216493), (0.872527, 0.197365, 0.446926)-76.683, 49.285, 38.174
4given(-0.493216, -0.156058, -0.855794), (0.011068, 0.982572, -0.185555), (0.869836, -0.100991, -0.482893)77.59, 15.888, 125.9
5given(-0.531383, -0.059496, -0.84504), (-0.06419, -0.991835, 0.110195), (-0.844696, 0.112799, 0.523225)73.594, 59.173, 36.637
DetailsTHE TRANSFORMATIONS PRESENTED ON *MTRIX* RECORDS BELOW CAN BE USED TO GENERATE THE COMPLETE HEXAMER.

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Components

#1: Protein
ARTHROPODAN HEMOCYANIN


Mass: 75696.203 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Panulirus interruptus (California spiny lobster)
References: UniProt: P04254
#2: 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.: 6
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)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPANULIRUS INTERRUPTUS HAEMOCYANIN HEXAMERS CONTAIN THREE DIFFERENT, THOUGH HOMOLOGOUS, SUBUNIT ...PANULIRUS INTERRUPTUS HAEMOCYANIN HEXAMERS CONTAIN THREE DIFFERENT, THOUGH HOMOLOGOUS, SUBUNIT TYPES. THE CRYSTALS USED FOR THE STRUCTURE DETERMINATION CONTAINED ABOUT EQUAL QUANTITIES OF SUBUNIT TYPES A AND B, WHICH DIFFER AT 18 POSITIONS. IN GENERAL THE SEQUENCE OF SUBUNIT TYPE A WAS FITTED TO THE DENSITY, EXCEPT FOR POSITIONS: 32, 163, 458 AND 514 WHERE THE SUBUNIT B SEQUENCE WAS USED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis / Details: referred to J.Mol.Biol. 99.619-629 / PH range low: 4.2 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 %hemocyanin11
20.05 Msodium acetate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
CORELSrefinement
PROLSQrefinement
RefinementResolution: 3.2→8 Å
Details: RESIDUES 1 - 4, 171 - 174, 551 - 552, 658 - 659 (THE TWO N-ACETYL GLUCOSAMINES) AND 34 WATER MOLECULES WITH TEMPERATURE FACTORS ABOVE 50 SHOULD BE CONSIDERED UNRELIABLE. IF THESE RESIDUES ...Details: RESIDUES 1 - 4, 171 - 174, 551 - 552, 658 - 659 (THE TWO N-ACETYL GLUCOSAMINES) AND 34 WATER MOLECULES WITH TEMPERATURE FACTORS ABOVE 50 SHOULD BE CONSIDERED UNRELIABLE. IF THESE RESIDUES AND WATERS ARE EXCLUDED FROM THE REFINEMENT, THE R-FACTOR BECOMES 0.224. THE REFINEMENT WAS CARRIED OUT BY FIRST MAINTAINING PERFECT 32 SYMMETRY, FOLLOWED BY RIGID BODY REFINEMENT OF THE 6 SUB UNITS, RESULTING IN A HEXAMER OF IDENTICAL SUB UNITS, BUT WITH SIGNIFICANT DEVIATIONS FROM 32 SYMMETRY (PROTEIN DATA BANK ENTRY 1HCY). SUBSEQUENT REFINEMENT RELAXING THE LOCAL SYMMETRY CONSTRAINTS RESULTED IN SIX NON-IDENTICAL MODELS (PROTEIN DATA BANK ENTRIES 1HC1 - 1HC6). NOTE THAT THE FOLLOWING DISTANCES ARE UNUSUALLY LARGE: C7 NAG 658 - C8 NAG 658 2.884 ANGSTROMS C7 NAG 659 - C8 NAG 659 3.140 ANGSTROMS
RfactorNum. reflection
obs0.221 59193
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31434 0 170 186 31790
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.031
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 8 Å / Num. reflection obs: 59193 / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.025
X-RAY DIFFRACTIONp_angle_d0.0450.094
X-RAY DIFFRACTIONp_planar_d0.0550.101
X-RAY DIFFRACTIONp_plane_restr0.020.028
X-RAY DIFFRACTIONp_chiral_restr0.20.29
X-RAY DIFFRACTIONp_mcbond_it1.51.9
X-RAY DIFFRACTIONp_scbond_it23.1
X-RAY DIFFRACTIONp_mcangle_it33.33
X-RAY DIFFRACTIONp_scangle_it45.4

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