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Basic information

Entry
Database: PDB / ID: 1iae
TitleCRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY
ComponentsASTACIN
KeywordsZINC ENDOPEPTIDASE
Function / homology
Function and homology information


astacin / glutamic-type peptidase activity / negative regulation of binding of sperm to zona pellucida / aspartic-type peptidase activity / prevention of polyspermy / cortical granule / positive regulation of protein processing / fertilization / metalloendopeptidase activity / peptidase activity ...astacin / glutamic-type peptidase activity / negative regulation of binding of sperm to zona pellucida / aspartic-type peptidase activity / prevention of polyspermy / cortical granule / positive regulation of protein processing / fertilization / metalloendopeptidase activity / peptidase activity / cell adhesion / proteolysis / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Astacin-like metallopeptidase domain / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. ...Astacin-like metallopeptidase domain / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Astacin
Similarity search - Component
Biological speciesAstacus astacus (noble crayfish)
MethodX-RAY DIFFRACTION / Resolution: 1.83 Å
AuthorsGrams, F. / Stoecker, W. / Bode, W.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: Crystal structures, spectroscopic features, and catalytic properties of cobalt(II), copper(II), nickel(II), and mercury(II) derivatives of the zinc endopeptidase astacin. A correlation of ...Title: Crystal structures, spectroscopic features, and catalytic properties of cobalt(II), copper(II), nickel(II), and mercury(II) derivatives of the zinc endopeptidase astacin. A correlation of structure and proteolytic activity.
Authors: Gomis-Ruth, F.X. / Grams, F. / Yiallouros, I. / Nar, H. / Kusthardt, U. / Zwilling, R. / Bode, W. / Stocker, W.
#1: Journal: FEBS Lett. / Year: 1993
Title: Astacins, Serralysins, Snake Venom and Matrix Metalloproteinases Exhibit Identical Zinc-Binding Environments (Hexxhxxgxxh and met-Turn) and Topologies and Should be Grouped Into a Common Family, the 'Metzincins'
Authors: Bode, W. / Gomis-Rueth, F.-X. / Stoecker, W.
#2: Journal: Nature / Year: 1992
Title: Structure of Astacin and Implications for Activation of Astacins and Zinc-Ligation of Collagenases
Authors: Bode, W. / Gomis-Rueth, F.X. / Huber, R. / Zwilling, R. / Stoecker, W.
History
DepositionMay 9, 1994Processing site: BNL
Revision 1.0Aug 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASTACIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6772
Polymers22,6181
Non-polymers591
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.890, 61.890, 98.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ASTACIN


Mass: 22617.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Astacus astacus (noble crayfish) / References: UniProt: P07584, astacin
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Details: taken from Gomis-Ruth(1993). J. Mol. Biol., 229, 945-968.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.3-0.6 mMprotein1drop0.005ml
21.1 Mammonium sulfate1drop0.0015ml
30.1 Mphosphate1drop
41 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.83 Å / Lowest resolution: 9.92 Å / Num. obs: 17177 / Num. measured all: 121292 / Rmerge(I) obs: 0.0443
Reflection shell
*PLUS
Highest resolution: 1.98 Å / Lowest resolution: 2.03 Å / % possible obs: 38.6 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.83→10 Å / Rfactor Rwork: 0.143 / Rfactor obs: 0.143
Refinement stepCycle: LAST / Resolution: 1.83→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 1 184 1776
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg2.282
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
Num. reflection obs: 16362 / Rfactor obs: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 5 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.282

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