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- PDB-1nol: OXYGENATED HEMOCYANIN (SUBUNIT TYPE II) -

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Basic information

Entry
Database: PDB / ID: 1nol
TitleOXYGENATED HEMOCYANIN (SUBUNIT TYPE II)
ComponentsHEMOCYANIN (SUBUNIT TYPE II)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


chloride ion binding / oxygen transport / oxygen carrier activity / oxidoreductase activity / copper ion binding / extracellular region
Similarity search - Function
Hemocyanin, N-terminal 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/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, C-terminal domain superfamily ...Hemocyanin, N-terminal 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/hexamerin middle domain / Hemocyanin, C-terminal / Hemocyanin, C-terminal domain superfamily / Hemocyanin, copper containing domain / Hemocyanin, ig-like domain / Hemocyanin/hexamerin / Hemocyanin, N-terminal domain / 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 / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / NITRATE ION / PEROXIDE ION / Hemocyanin II
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsHazes, B. / Hol, W.G.J.
Citation
Journal: Protein Sci. / Year: 1993
Title: Crystal structure of deoxygenated Limulus polyphemus subunit II hemocyanin at 2.18 A resolution: clues for a mechanism for allosteric regulation.
Authors: Hazes, B. / Magnus, K.A. / Bonaventura, C. / Bonaventura, J. / Dauter, Z. / Kalk, K.H. / Hol, W.G.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Hexameric Haemocyanin from Panulirus Interruptus Refined at 3.2 Angstroms Resolution
Authors: Volbeda, A. / Hol, W.G.J.
#2: Journal: J.Biol.Chem. / Year: 1986
Title: Structure of Hemocyanin II from the Horseshoe Crab, Limulus Polyphemus
Authors: Nakashima, H. / Behrens, P.Q. / Moore, M.D. / Yokota, E. / Riggs, A.F.
History
DepositionOct 17, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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.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.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

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Assembly

Deposited unit
A: HEMOCYANIN (SUBUNIT TYPE II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0196
Polymers72,7581
Non-polymers2615
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.002, 117.002, 117.002
Angle α, β, γ (deg.)60.02, 60.02, 60.02
Int Tables number155
Space group name H-MR32
Atom site foot note1: GLU 309 - SER 310 OMEGA = 356.79 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLY 525 - LEU 526 OMEGA = 113.53 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO 599
DetailsBIOLOGICAL UNIT THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 1 .. 633 A HEMOCYANIN HEXAMER IS OBTAINED BY APPLYING THE CRYSTALLOGRAPHIC SYMMETRY OPERATORS. HOWEVER, ONE SHOULD REMEMBER THAT IN THE BIOLOGICAL MOLECULE THERE ARE 8 OF THESE HEXAMERS AND THAT EACH HEXAMER CONSISTS OF SEVERAL CHAINS WITH RELATED BUT DIFFERENT AMINO ACID SEQUENCES. SYMMETRY1 1 0.000000 0.000000 1.000000 0.00000 SYMMETRY2 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY1 2 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 2 0.000000 0.000000 1.000000 0.00000 SYMMETRY3 2 1.000000 0.000000 0.000000 0.00000 SYMMETRY1 3 0.000000 -1.000000 0.000000 0.00000 SYMMETRY2 3 -1.000000 0.000000 0.000000 0.00000 SYMMETRY3 3 0.000000 0.000000 -1.000000 0.00000 SYMMETRY1 4 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 4 0.000000 0.000000 -1.000000 0.00000 SYMMETRY3 4 0.000000 -1.000000 0.000000 0.00000 SYMMETRY1 5 0.000000 0.000000 -1.000000 0.00000 SYMMETRY2 5 0.000000 -1.000000 0.000000 0.00000 SYMMETRY3 5 -1.000000 0.000000 0.000000 0.00000

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HEMOCYANIN (SUBUNIT TYPE II)


Mass: 72757.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Limulus polyphemus (Atlantic horseshoe crab)
Tissue: HEMOLYMPH / References: UniProt: P04253

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Non-polymers , 5 types, 217 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE STRUCTURE IS BELIEVED TO REPRESENT AN OXYGENATED LOW OXYGEN AFFINITY (OR T-STATE) CONFORMATION.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growPH range: 6.5-7.0
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→33.8 Å / Num. obs: 24861 / % possible obs: 83.7 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
MADNES/KABSCHPROFILESdata collection
X-PLOR2.1model building
X-PLOR2.1refinement
MADNESdata reduction
KABSCHdata reduction
PROFILESdata reduction
X-PLOR2.1phasing
RefinementResolution: 2.4→8 Å / σ(F): 0
Details: THE NON-STANDARD RHOMBOHEDRAL SETTING OF R 3 2 WAS USED.
RfactorNum. reflection% reflection
Rwork0.181 --
obs0.181 24024 83.4 %
Displacement parametersBiso mean: 16.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4933 0 9 212 5154
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.50.5
X-RAY DIFFRACTIONx_mcangle_it11
X-RAY DIFFRACTIONx_scbond_it11
X-RAY DIFFRACTIONx_scangle_it22

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