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- PDB-1qji: Structure of astacin with a transition-state analogue inhibitor -

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Basic information

Entry
Database: PDB / ID: 1qji
TitleStructure of astacin with a transition-state analogue inhibitor
ComponentsASTACIN
KeywordsHYDROLASE(METALLOPROTEINASE) / ASTACINS / METZINCINS
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
CARBOBENZOXY-PRO-LYS-PHE-Y(PO2)-ALA-PRO-OME / Astacin
Similarity search - Component
Biological speciesASTACUS FLUVIATILIS (noble crayfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsGrams, F. / Bode, W. / Stocker, W.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: Structure of Astacin with a Transition-State Analogue Inhibitor
Authors: Grams, F. / Dive, V. / Yiotakis, A. / Yiallouros, I. / Vassiliou, S. / Zwilling, R. / Bode, W. / Stocker, W.
History
DepositionJun 24, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: ASTACIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4273
Polymers22,6181
Non-polymers8092
Water2,972165
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.170, 61.170, 99.560
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 / CRAYFISH SMALL MOLECULE PROTEINASE


Mass: 22617.977 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Source method: isolated from a natural source
Details: IN COMPLEX WITH A BOUND TRANSITION-STATE ANALOGUE PHOSPHINIC PSEUDOPEPTIDE CARBOBENZOXY-PRO-LYS-PHE-Y(PO2)-ALA-PRO-OME
Source: (natural) ASTACUS FLUVIATILIS (noble crayfish) / Cell: F-CELL / Organ: MIDGUT GLAND / Secretion: DIGESTIVE FLUID / References: UniProt: P07584, astacin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PKF / CARBOBENZOXY-PRO-LYS-PHE-Y(PO2)-ALA-PRO-OME


Mass: 743.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H52N6O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CDNA ENCODES TWO ADDITIONAL C-TERMINAL RESIDUES ARG-HIS THAT ARE CLEAVED OFF ...THE CDNA ENCODES TWO ADDITIONAL C-TERMINAL RESIDUES ARG-HIS THAT ARE CLEAVED OFF POSTTRANSLATIONALLY AND NOT PRESENT IN THE PROTEIN STUDIED
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP VAPOUR DIFFUSION PH 7.0, 1M AMMONIUM SULFATE
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Gomiz-Ruth, F.-W., (1993) J. Mol. Biol., 229, 945. / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.3-0.6 mMprotein1drop
21.1 Mammonium sulfate1drop
30.1 Mphosphate1droppH7.0
41 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 2.14
DetectorType: BRUKER NONIUS FAST / Detector: AREA DETECTOR / Date: Jun 15, 1994 / Details: COLLIMATOR PINHOLES
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.14 Å / Relative weight: 1
ReflectionResolution: 2.14→8 Å / Num. obs: 12071 / % possible obs: 77.6 % / Observed criterion σ(I): 0.6 / Redundancy: 2.5 % / Rmerge(I) obs: 0.109
Reflection shellResolution: 2.14→2.19 Å / % possible all: 30.4
Reflection
*PLUS
Num. measured all: 39277
Reflection shell
*PLUS
% possible obs: 30.4 %

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Processing

Software
NameClassification
X-PLORrefinement
MADNESSdata reduction
PROTEINdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AST

1ast


Resolution: 2.14→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.164 --
obs0.164 7942 70 %
Displacement parametersBiso mean: 27.44 Å2
Refinement stepCycle: LAST / Resolution: 2.14→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1590 0 53 165 1808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.7
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: 9366
Solvent computation
*PLUS
Displacement parameters
*PLUS

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