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- PDB-1iac: REFINED 1.8 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF ASTACIN, A ZINC-... -

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Entry
Database: PDB / ID: 1iac
TitleREFINED 1.8 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF ASTACIN, A ZINC-ENDOPEPTIDASE FROM THE CRAYFISH ASTACUS ASTACUS L. STRUCTURE DETERMINATION, REFINEMENT, MOLECULAR STRUCTURE AND COMPARISON WITH THERMOLYSIN
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
Biological speciesAstacus astacus (noble crayfish)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsGomis-Rueth, F.-X. / Stoecker, W. / Bode, W.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Refined 1.8 A X-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish Astacus astacus L. Structure determination, refinement, molecular structure and comparison with thermolysin.
Authors: Gomis-Ruth, F.X. / Stocker, W. / Huber, R. / Zwilling, R. / Bode, W.
#1: 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-Rueth, F.-X. / Grams, F. / Yiallouros, I. / Nar, H. / Kuesthardt, U. / Zwilling, R. / Bode, W. / Stoecker, W.
#2: 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.
#3: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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.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 1.4Oct 23, 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)22,8192
Polymers22,6181
Non-polymers2011
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.920, 61.920, 98.570
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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 48.99 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
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
Num. obs: 10213 / % possible obs: 98.57 % / Num. measured all: 27702 / Rmerge(I) obs: 0.0847
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.13 Å / % possible obs: 46.5 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→10 Å / Rfactor Rwork: 0.16 / Rfactor obs: 0.16
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1591 0 1 172 1764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.271
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: 10039 / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.271

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