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- PDB-1n8o: Crystal structure of a complex between bovine chymotrypsin and ecotin -

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Basic information

Entry
Database: PDB / ID: 1n8o
TitleCrystal structure of a complex between bovine chymotrypsin and ecotin
Components
  • Chymotrypsin A, A chain
  • Chymotrypsin A, C chain
  • Chymotrypsin A, b chain
  • ecotin
KeywordsHYDROLASE
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / protein homodimerization activity / proteolysis / extracellular region
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
Chymotrypsinogen A / Ecotin
Similarity search - Component
Biological speciesBos taurus (cattle)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCambillau, C. / Spinelli, S. / Lauwereys, M.
CitationJournal: To be Published
Title: Crystal Structure of a Complex Between Bovine Chymotrypsin and Ecotin at 2.0 A Resolution
Authors: Cambillau, C. / Spinelli, S. / Lauwereys, M.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 1.5Apr 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chymotrypsin A, A chain
B: Chymotrypsin A, b chain
C: Chymotrypsin A, C chain
E: ecotin


Theoretical massNumber of molelcules
Total (without water)41,3834
Polymers41,3834
Non-polymers00
Water3,909217
1
A: Chymotrypsin A, A chain
B: Chymotrypsin A, b chain
C: Chymotrypsin A, C chain
E: ecotin

A: Chymotrypsin A, A chain
B: Chymotrypsin A, b chain
C: Chymotrypsin A, C chain
E: ecotin


Theoretical massNumber of molelcules
Total (without water)82,7668
Polymers82,7668
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Unit cell
Length a, b, c (Å)95.5, 63.8, 79.6
Angle α, β, γ (deg.)90, 91.7, 90
Int Tables number4
Space group name H-MP1211
DetailsThe complex between dimeric ecotin and 2 chymotrysins is generated by crystal symmetry

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Components

#1: Protein/peptide Chymotrypsin A, A chain


Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein Chymotrypsin A, b chain


Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#3: Protein Chymotrypsin A, C chain


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#4: Protein ecotin /


Mass: 16120.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P23827
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Ammonium sulfate 1.3M, Sodium Acetate 0.1M, 1% PEG 200, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 1993
RadiationMonochromator: Graphite mono-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 30343 / Num. obs: 30343 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.065
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.27 / % possible all: 67

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bovine Chymotrypsin, Ecotin

Resolution: 2→30 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rwork0.205 -
obs0.205 30343
Rfree-1254
all-30343
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 0 217 3009
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0017
X-RAY DIFFRACTIONx_angle_d1.89

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