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- PDB-1acb: CRYSTAL AND MOLECULAR STRUCTURE OF THE BOVINE ALPHA-CHYMOTRYPSIN-... -

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Basic information

Entry
Database: PDB / ID: 1acb
TitleCRYSTAL AND MOLECULAR STRUCTURE OF THE BOVINE ALPHA-CHYMOTRYPSIN-EGLIN C COMPLEX AT 2.0 ANGSTROMS RESOLUTION
Components
  • ALPHA-CHYMOTRYPSINChymotrypsin
  • Eglin C
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyPeptidase S1, PA clan / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin domain profile. / Potato inhibitor I family signature. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin family, histidine active site. / Potato inhibitor I family / Trypsin / Proteinase inhibitor I13, potato inhibitor I / Serine proteases, trypsin domain ...Peptidase S1, PA clan / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin domain profile. / Potato inhibitor I family signature. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin family, histidine active site. / Potato inhibitor I family / Trypsin / Proteinase inhibitor I13, potato inhibitor I / Serine proteases, trypsin domain / Peptidase S1A, chymotrypsin family / Proteinase inhibitor I13, potato inhibitor I superfamily / Serine proteases, trypsin family, histidine active site / chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / response to wounding / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / extracellular space / Chymotrypsinogen A / Eglin C
Function and homology information
Specimen sourceBos taurus (cattle)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / 2 Å resolution
AuthorsBolognesi, M. / Frigerio, F. / Coda, A. / Pugliese, L. / Lionetti, C. / Menegatti, E. / Amiconi, G. / Schnebli, H.P. / Ascenzi, P.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Crystal and molecular structure of the bovine alpha-chymotrypsin-eglin c complex at 2.0 A resolution.
Authors: Frigerio, F. / Coda, A. / Pugliese, L. / Lionetti, C. / Menegatti, E. / Amiconi, G. / Schnebli, H.P. / Ascenzi, P. / Bolognesi, M.
#1: Journal: J.Mol.Recog. / Year: 1990
Title: X-Ray Crystal Structure of the Bovine Alpha-Chymotrypsin(Slash)Eglin C Complex at 2.6 Angstroms Resolution
Authors: Bolognesi, M. / Pugliese, L. / Gatti, G. / Frigerio, F. / Coda, A. / Antolini, L. / Schnebli, H.P. / Menegatti, E. / Amiconi, G. / Ascenzi, P.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Preliminary Crystallographic Data on the Complex of Bovine Alpha-Chymotrypsin with the Recombinant Proteinase Inhibitor Eglin C from Hirudo Medicinalis
Authors: Pugliese, L. / Gatti, G. / Bolognesi, M. / Coda, A. / Menegatti, E. / Schnebli, H.P. / Ascenzi, P. / Amiconi, G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 8, 1991 / Release: Oct 31, 1993
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 31, 1993Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Nov 29, 2017Structure modelAdvisory / Derived calculations / Otherpdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type_pdbx_database_status.process_site
Remark 700SHEET THE SHEETS PRESENTED AS *CH1* AND *CH2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED ...SHEET THE SHEETS PRESENTED AS *CH1* AND *CH2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY SEVEN-STRANDED SHEETS 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
E: ALPHA-CHYMOTRYPSIN
I: Eglin C


Theoretical massNumber of molelcules
Total (without water)33,7862
Polyers33,7862
Non-polymers00
Water2,558142
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)1540
ΔGint (kcal/M)-12
Surface area (Å2)13180
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)55.300, 59.400, 42.500
Angle α, β, γ (deg.)90.00, 99.10, 90.00
Int Tables number4
Space group name H-MP 1 21 1
Atom site foot note1: RESIDUES WITH POOR ELECTRON DENSITY: SER E 77, GLU E 78, ARG E 145, ALA E 149, ASN E 150, ARG E 154, GLN E 239, LYS I 8, HIS I 28, TYR I 49, ASN I 50.

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Components

#1: Protein/peptide ALPHA-CHYMOTRYPSIN / Chymotrypsin


Mass: 25686.037 Da / Num. of mol.: 1 / Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein/peptide Eglin C


Mass: 8100.011 Da / Num. of mol.: 1 / Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / References: UniProt: P01051
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Formula: H2O / Water
Compound detailsEGLIN C IS BOUND NON-COVALENTLY TO THE ACTIVE SITE OF THE ENZYME.
Sequence detailsRESIDUES THR I 1, GLU I 2, PHE I 3, GLY I 4, SER I 5, GLU I 6, AND LEU I 7 OF EGLIN C HAVE BEEN ...RESIDUES THR I 1, GLU I 2, PHE I 3, GLY I 4, SER I 5, GLU I 6, AND LEU I 7 OF EGLIN C HAVE BEEN PROTEOLYTICALLY CLEAVED BY THE ENZYME DURING CRYSTALLIZATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 / Density percent sol: 39.68 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop / Details: referred to J.Mol.Biol. 208.511-513
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDDetails
115 mg/mlalpha chymotrypsin1drop
27 mg/mleglin c1drop
30.05 Mphosphate1drop
45 %(w/v)PEG40001dropcan be replaced with PEG6000
510 %PEG40001reservoircan be replaced with PEG6000

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2 Å / D resolution low: 11 Å / Number obs: 16841 / Number measured all: 31318 / Rmerge I obs: 0.04 / Observed criterion sigma I: 5

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Processing

SoftwareName: TNT / Classification: refinement
RefineSigma F: 0
Least-squares processR factor obs: 0.167 / Highest resolution: 2 Å / Lowest resolution: 11 Å
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 11 Å
Number of atoms included #LASTProtein: 2289 / Nucleic acid: 0 / Ligand: 0 / Solvent: 142 / Total: 2431
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.97
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.018
X-RAY DIFFRACTIONt_gen_planes0.019
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.086
Refine
*PLUS
Sigma F: 0
Least-squares process
*PLUS
R factor all: 0.167 / Highest resolution: 2 Å / Lowest resolution: 11 Å / Number reflection all: 16833
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.019

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