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- PDB-1ab9: CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN -

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Entry
Database: PDB / ID: 1ab9
TitleCRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN
DescriptorGAMMA-CHYMOTRYPSIN, PENTAPEPTIDE (TPGVY)
KeywordsCOMPLEX (SERINE PROTEASE/PEPTIDE) / HYDROLASE / SERINE PROTEASE / DIGESTION / PANCREAS / ZYMOGEN / COMPLEX (SERINE PROTEASE-PEPTIDE) / COMPLEX (SERINE PROTEASE-PEPTIDE) complex
Specimen sourceBos taurus / mammal / cattle / ウシ /
MethodX-ray diffraction (1.6 Å resolution / Molecular replacement)
AuthorsSugio, S. / Kashima, A. / Inoue, Y. / Maeda, I. / Nose, T. / Shimohigashi, Y.
CitationEur.J.Biochem., 1998, 255, 12-23

primary. Eur.J.Biochem., 1998, 255, 12-23 Yorodumi Papers
X-ray crystal structure of a dipeptide-chymotrypsin complex in an inhibitory interaction.
Kashima, A. / Inoue, Y. / Sugio, S. / Maeda, I. / Nose, T. / Shimohigashi, Y.

#1. Biochemistry, 1991, 30, 5217-
Gamma-Chymotrypsin is a Complex of Alpha-Chymotrypsin with its Own Autolysis Products
Harel, M. / Su, C.T. / Frolow, F. / Silman, I. / Sussman, J.L.

#2. Int.J.Biol.Macromol., 1991, 13, 89-
Structure of Gamma-Chymotrypsin in the Range Ph 2.0 To Ph 10.5 Suggests that Gamma-Chymotrypsin is a Covalent Acyl-Enzyme Adduct at Low Ph
Dixon, M.M. / Brennan, R.G. / Matthews, B.W.

#3. Biochemistry, 1989, 28, 7033-
Is Gamma-Chymotrypsin a Tetrapeptide Acyl-Enzyme Adduct of Alpha-Chymotrypsin?
Dixon, M.M. / Matthews, B.W.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 5, 1997 / Release: Aug 20, 1997
RevisionDateData content typeGroupProviderType
1.0Aug 20, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Dec 12, 2012Structure modelOther
1.4Mar 13, 2013Structure modelOther

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Structure visualization

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Assembly

Deposited unit
A: GAMMA-CHYMOTRYPSIN
B: GAMMA-CHYMOTRYPSIN
C: GAMMA-CHYMOTRYPSIN
D: PENTAPEPTIDE (TPGVY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8945
Polyers25,7984
Non-polymers961
Water2,288127
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7950
ΔGint (kcal/M)-76
Surface area (Å2)10230
MethodPISA
#2
A: GAMMA-CHYMOTRYPSIN
B: GAMMA-CHYMOTRYPSIN
C: GAMMA-CHYMOTRYPSIN
D: PENTAPEPTIDE (TPGVY)
hetero molecules

A: GAMMA-CHYMOTRYPSIN
B: GAMMA-CHYMOTRYPSIN
C: GAMMA-CHYMOTRYPSIN
D: PENTAPEPTIDE (TPGVY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,78810
Polyers51,5968
Non-polymers1922
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area (Å2)18470
ΔGint (kcal/M)-175
Surface area (Å2)17880
MethodPISA
#3
A: GAMMA-CHYMOTRYPSIN

A: GAMMA-CHYMOTRYPSIN

B: GAMMA-CHYMOTRYPSIN
C: GAMMA-CHYMOTRYPSIN
D: PENTAPEPTIDE (TPGVY)
hetero molecules

B: GAMMA-CHYMOTRYPSIN
C: GAMMA-CHYMOTRYPSIN
D: PENTAPEPTIDE (TPGVY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,78810
Polyers51,5968
Non-polymers1922
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation5_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation6_555x+1/2,-y+1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area (Å2)17130
ΔGint (kcal/M)-160
Surface area (Å2)19230
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)69.520, 69.520, 97.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP 42 21 2

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Components

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Polypeptide(L) , 4 types, 4 molecules ABCD

#1: Polypeptide(L)GAMMA-CHYMOTRYPSIN


Mass: 1253.511 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: P00766, EC: 3.4.21.1

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)GAMMA-CHYMOTRYPSIN


Mass: 13934.556 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: P00766, EC: 3.4.21.1

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)GAMMA-CHYMOTRYPSIN


Mass: 10074.495 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: P00766, EC: 3.4.21.1

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)PENTAPEPTIDE (TPGVY)


Mass: 535.590 Da / Num. of mol.: 1

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Non-polymers , 2 types, 128 molecules

#5: ChemicalChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4
#6: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Formula: H2O

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Details

Compound detailsTHE BOUND PENTAPEPTIDE (THR D 300 TO TYR D 304) HAVE TWO DIFFERENT CONFORMATIONS. THE OCCUPANCIES OF ALL THE ATOMS IN THE PEPTIDE WERE SET TO 0.5.

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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: 2.29 / Density percent sol: 46.28
Crystal growMethod: VAPOR DIFFUSION, SITTING DROP / pH: 5.6
Details: ALPHA-CHYMOTRYPSIN WAS DISSOLVED IN POTASSIUM BORATE (PH8.6) AND WAS INCUBATED AT 310K FOR 6 HOURS. SOLID AMMONIUM SULFATE WAS ADDED TO THE SOLUTION, AND THE PRECIPITATE FORMED WAS RECOVERED AND RE-DISSOLVED WITH WATER. CRYSTALLIZATION WAS DONE WITH A SITTING-DROP VAPOR-DIFFUSION PROCEDURE, IN WHICH PROTEIN SOLUTION (15MG/ML) CONTAINING 10MM CACODYLATE, 0.75% SATURATED ACETYLTRIMETHYL AMMONIUM AND 45% SATURATED AMMONIUM SULFATE WAS EQUILIBRATED AGAINST 65% SATURATED AMMONIUM SULFATE AT 293K., pH 5.6, vapor diffusion - sitting drop
Crystal grow
*PLUS
Temp unit: K / Method: Vapor diffusion
Crystal grow comp
*PLUS
IDConcConc unitCrystal IDCommon nameSol ID
115mg/ml1chymotrypsindrop
210mM1sodium cacodylatedrop
30.75%sat1cetyltrimethylammonium bromidedrop
445%sat1ammonium sulfatedrop
565%sat1ammonium sulfatereservoir

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Data collection

DiffractionMean temperature: 292 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Details: YALE MIRRORS / Detector: IMAGE PLATE / Collection date: Oct 24, 1995
RadiationMonochromator: NI FILTER / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 19 Å2 / D resolution high: 1.6 Å / D resolution low: 69.5 Å / Number obs: 31740 / Observed criterion sigma I: 1 / Rmerge I obs: 0.055 / NetI over sigmaI: 15.1 / Redundancy: 10.3 / Percent possible obs: 97.8
Reflection shellRmerge I obs: 0.208 / Highest resolution: 1.6 Å / Lowest resolution: 1.65 Å / MeanI over sigI obs: 3.1 / Percent possible all: 94.7
Reflection
*PLUS
Number measured all: 332021
Reflection shell
*PLUS
Percent possible obs: 94.7

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Processing

Software
NameVersionClassification
CONTROLdata collection
PROCESSdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CONTROLdata reduction
PROCESSdata scaling
X-PLOR3.1phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCT
Details: THE FOLLOWING WEIGHTING SCHEME WAS USED: 1/(SIGMAF)**2 SIDE CHAINS OF VAL B 53 AND GLN C 239 HAVE ALTERNATE CONFORMATIONS. THE OCCUPANCIES OF THE CORRESPONDING ATOMS WERE SET TO 0.5.
R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: POSTERIORI / Sigma F: 2
Displacement parametersB iso mean: 21.2 Å2
Least-squares processR factor R free: 0.19 / R factor R free error: 0.004 / R factor R work: 0.191 / R factor obs: 0.191 / Highest resolution: 1.6 Å / Lowest resolution: 5 Å / Number reflection R free: 2496 / Number reflection obs: 30329 / Percent reflection R free: 8 / Percent reflection obs: 97.3
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å
Refine hist #LASTHighest resolution: 1.6 Å / Lowest resolution: 5 Å
Number of atoms included #LASTProtein: 1821 / Nucleic acid: 0 / Ligand: 5 / Solvent: 127 / Total: 1953
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.50
X-RAY DIFFRACTIONx_mcangle_it2.00
X-RAY DIFFRACTIONx_scbond_it2.00
X-RAY DIFFRACTIONx_scangle_it2.50
Refine LS shellHighest resolution: 1.6 Å / R factor R free: 0.263 / R factor R free error: 0.017 / R factor R work: 0.285 / Lowest resolution: 1.66 Å / Number reflection R free: 243 / Number reflection R work: 2630 / Total number of bins used: 10 / Percent reflection R free: 8 / Percent reflection obs: 93.4
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.PARTOPOL.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26
Refine LS shell
*PLUS
R factor obs: 0.285

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