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- PDB-1lla: CRYSTAL STRUCTURE OF DEOXYGENATED LIMULUS POLYPHEMUS SUBUNIT II H... -

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Basic information

Entry
Database: PDB / ID: 1lla
TitleCRYSTAL STRUCTURE OF DEOXYGENATED LIMULUS POLYPHEMUS SUBUNIT II HEMOCYANIN AT 2.18 ANGSTROMS RESOLUTION: CLUES FOR A MECHANISM FOR ALLOSTERIC REGULATION
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 / Hemocyanin II
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / Resolution: 2.18 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: Proteins / Year: 1991
Title: Hexamers of Subunit II from Limulus Hemocyanin (A 48-mer) Have the Same Quaternary Structure as Whole Panulirus Hemocyanin Molecules
Authors: Magnus, K.A. / Lattman, E.E. / Volbeda, A. / Hol, W.G.J.
#2: 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.
#3: Journal: J.Biol.Chem. / Year: 1986
Title: Structure of Hemocyanin II from the Horshoe Crab Limulus Polyphemus
Authors: Nakashima, H. / Behrens, P.Q. / Moore, M.D. / Yokota, E. / Riggs, A.F.
History
DepositionSep 7, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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.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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)72,9435
Polymers72,7581
Non-polymers1864
Water5,981332
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: RESIDUE PRO 599 IS A CIS PROLINE.

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Components

#1: Protein HEMOCYANIN (SUBUNIT TYPE II)


Mass: 72757.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limulus polyphemus (Atlantic horseshoe crab)
References: UniProt: P04253
#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBASED ON OXYGEN BINDING STUDIES THAT MIMIC THE CRYSTALLIZATION CONDITIONS THE STRUCTURE IS BELIEVED ...BASED ON OXYGEN BINDING STUDIES THAT MIMIC THE CRYSTALLIZATION CONDITIONS THE STRUCTURE IS BELIEVED TO REPRESENT THE LOW OXYGEN AFFINITY (OR T-STATE) CONFORMATION.
Has protein modificationY
Sequence detailsSEQUENCE ADVISORY NOTICE: THE SEQUENCE HAS BEEN CHANGED IN THREE POSITIONS COMPARED TO THE ...SEQUENCE ADVISORY NOTICE: THE SEQUENCE HAS BEEN CHANGED IN THREE POSITIONS COMPARED TO THE PUBLISHED SEQUENCE (NAKASHIMA, 1986). DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: HCY2_LIMPO SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE VAL 9 ILE 9 PHE 408 THR 408 THR 409 PHE 409

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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 grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Details: taken from mangus, K.A. et al (1991). Proteins Struct. Funct. Genet., 9, 240-247.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1160 mMBis Tris1reservoir
230 mMTris-HCl1reservoir
330 mMglycine1reservoir
46 mMEDTA1reservoir
54 %PEG80001reservoir
60.5 M1reservoirNaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.18 Å / % possible obs: 97 % / Num. measured all: 38255 / Rmerge(I) obs: 0.046

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.18→10 Å / Rfactor Rwork: 0.174 / Rfactor obs: 0.174 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.18→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 4 332 5196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.9
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.18 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor all: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.9

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