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- PDB-1azz: FIDDLER CRAB COLLAGENASE COMPLEXED TO ECOTIN -

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Basic information

Entry
Database: PDB / ID: 1azz
TitleFIDDLER CRAB COLLAGENASE COMPLEXED TO ECOTIN
Components
  • COLLAGENASE
  • ECOTIN
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) / SERINE PROTEASE / INHIBITOR / COMPLEX / PROTEASE-SUBSTRATE INTERACTIONS / COLLAGEN / COMPLEX (SERINE PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


brachyurin / collagen catabolic process / serine-type endopeptidase inhibitor activity / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / protein homodimerization activity
Similarity search - Function
Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. ...Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCeluca pugilator (Atlantic sand fiddler crab)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsPerona, J.J. / Fletterick, R.J.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structure of an ecotin-collagenase complex suggests a model for recognition and cleavage of the collagen triple helix.
Authors: Perona, J.J. / Tsu, C.A. / Craik, C.S. / Fletterick, R.J.
#1: Journal: Embo J. / Year: 1994
Title: Macromolecular Chelation as an Improved Mechanism of Protease Inhibition: Structure of the Ecotin-Trypsin Complex
Authors: Mcgrath, M.E. / Erpel, T. / Bystroff, C. / Fletterick, R.J.
History
DepositionNov 24, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLLAGENASE
B: COLLAGENASE
C: ECOTIN
D: ECOTIN


Theoretical massNumber of molelcules
Total (without water)79,2814
Polymers79,2814
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-54 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.110, 89.110, 291.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein COLLAGENASE


Mass: 23520.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CRAB HEPATOPANCREAS
Source: (natural) Celuca pugilator (Atlantic sand fiddler crab)
References: UniProt: P00771, brachyurin
#2: Protein ECOTIN / TRYPSIN INHIBITOR


Mass: 16120.507 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Plasmid: PTACTAC / References: UniProt: P23827
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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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: 4.2 Å3/Da / Density % sol: 72 %
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 8.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Msodium citrate1reservoir
240 %PEG40001reservoir
30.2 Mtricine1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 41721 / % possible obs: 78 % / Redundancy: 3 % / Rmerge(I) obs: 0.095
Reflection
*PLUS
Num. measured all: 109981

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Processing

Software
NameVersionClassification
R-AXISdata collection
R-AXISdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.3→6 Å /
Rfactor% reflection
Rfree0.238 10 %
Rwork0.189 -
obs0.189 -
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5387 0 0 140 5527
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_deg2.8
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
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2

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