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- PDB-2y6t: Molecular Recognition of Chymotrypsin by the Serine Protease Inhi... -

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Basic information

Entry
Database: PDB / ID: 2y6t
TitleMolecular Recognition of Chymotrypsin by the Serine Protease Inhibitor Ecotin from Yersinia pestis
Components
  • CHYMOTRYPSINOGEN A
  • ECOTIN
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / periplasmic space / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Ecotin / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. ...Ecotin / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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 / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ecotin / Chymotrypsinogen A
Similarity search - Component
Biological speciesYERSINIA PSEUDOTUBERCULOSIS (bacteria)
BOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsClark, E.A. / Walker, N. / Ford, D.C. / Cooper, I.A. / Oyston, P.C.F. / Acharya, K.R.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular Recognition of Chymotrypsin by the Serine Protease Inhibitor Ecotin from Yersinia Pestis.
Authors: Clark, E.A. / Walker, N. / Ford, D.C. / Cooper, I.A. / Oyston, P.C. / Acharya, K.R.
History
DepositionJan 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 29, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHYMOTRYPSINOGEN A
B: CHYMOTRYPSINOGEN A
C: CHYMOTRYPSINOGEN A
D: CHYMOTRYPSINOGEN A
E: ECOTIN
F: ECOTIN
G: ECOTIN
H: ECOTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,11712
Polymers169,7338
Non-polymers3844
Water59433
1
A: CHYMOTRYPSINOGEN A
B: CHYMOTRYPSINOGEN A
E: ECOTIN
F: ECOTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0596
Polymers84,8664
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-82 kcal/mol
Surface area32920 Å2
MethodPISA
2
C: CHYMOTRYPSINOGEN A
D: CHYMOTRYPSINOGEN A
G: ECOTIN
H: ECOTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0596
Polymers84,8664
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9570 Å2
ΔGint-84.1 kcal/mol
Surface area32330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.310, 48.278, 174.636
Angle α, β, γ (deg.)90.00, 103.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CHYMOTRYPSINOGEN A / CHYMOTRYPSIN


Mass: 25686.037 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: ACTIVATED BOVINE CHYMOTRYPSIN WAS PURCHASED FROM SIGMA-ALDRICH
Source: (natural) BOS TAURUS (domestic cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein
ECOTIN


Mass: 16747.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PSEUDOTUBERCULOSIS (bacteria) / Strain: YPIII / Plasmid: PCRT7/NT-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: B1JSA0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.5 % / Description: NONE
Crystal growpH: 5.5
Details: RESERVOIR SOLUTION - 100 MM BIS TRIS PH 5.5, 200 MM AMMONIUM SULPHATE, 17.5% PEG3350. PROTEIN SOLUTION - 3 MG/ML ECOTIN, 6 MG/ML CHYMOTRYPSIN IN 5MM TRIS PH 7.5. DROP - 1:1 VOLUME RATIO RESERVOIR:PROTEIN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 20, 2010 / Details: MIRRORS
RadiationMonochromator: SI (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.74→169.48 Å / Num. obs: 42247 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.27
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.51 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4CHA AND 1ECZ

4cha

1ecz


Resolution: 2.74→169.48 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.824 / SU B: 18.243 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.31444 2080 5.1 %RANDOM
Rwork0.24386 ---
obs0.24741 39088 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20.12 Å2
2--1.83 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.74→169.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11476 0 20 33 11529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211733
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9521.95215957
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41351501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50625.168447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.948151958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0261544
X-RAY DIFFRACTIONr_chiral_restr0.060.21825
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218680
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3031.57525
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.562212137
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.52134208
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9274.53820
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.739→2.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 147 -
Rwork0.32 2756 -
obs--93.68 %

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