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- PDB-1qjj: Structure of astacin with a hydroxamic acid inhibitor -

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Basic information

Entry
Database: PDB / ID: 1qjj
TitleStructure of astacin with a hydroxamic acid inhibitor
Components
  • ASTACIN
  • PRO-LEU-GLY-HYDROXAMIC ACID
KeywordsHYDROLASE/HYDROLASE INHIBITOR / METALLOPROTEINASE / ASTACINS / METZINCINS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
L-prolyl-L-leucyl-N-hydroxyglycinamide / Astacin
Similarity search - Component
Biological speciesASTACUS FLUVIATILIS (noble crayfish)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 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 24, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Dec 28, 2016Group: Source and taxonomy
Revision 1.4Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Jul 12, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.name
Revision 1.6May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.7Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _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

Downloads & links

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Assembly

Deposited unit
A: ASTACIN
B: PRO-LEU-GLY-HYDROXAMIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9843
Polymers22,9182
Non-polymers651
Water3,189177
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-43 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.900, 61.900, 98.700
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 / Source: (natural) ASTACUS FLUVIATILIS (noble crayfish) / Cell: F-CELL / Organ: MIDGUT GLAND / Secretion: DIGESTIVE FLUID / References: UniProt: P07584, astacin
#2: Protein/peptide PRO-LEU-GLY-HYDROXAMIC ACID


Type: Peptide-like / Class: Inhibitor / Mass: 300.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: L-prolyl-L-leucyl-N-hydroxyglycinamide
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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

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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: 48.36 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP VAPOUR DIFFUSION PH 7.0, 1M AMMONIUM SULFATE
Crystal grow
*PLUS
Method: unknown
Details: This particular structure is not described in this paper.

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.86
DetectorType: BRUKER NONIUS FAST / Detector: AREA DETECTOR / Date: May 15, 1994 / Details: COLLIMATOR PINHOLES
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.86 Å / Relative weight: 1
ReflectionResolution: 1.86→8 Å / Num. obs: 16311 / % possible obs: 67.8 % / Observed criterion σ(I): 0.6 / Redundancy: 2.5 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 1.86→1.9 Å / % possible all: 35.5

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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: 1.86→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.161 --
obs0.161 12506 70 %
Displacement parametersBiso mean: 10.18 Å2
Refinement stepCycle: LAST / Resolution: 1.86→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 1 177 1790
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.5
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

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