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- PDB-5j4s: alpha-chymotrypsin from bovine pancreas in complex with a modifie... -

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Basic information

Entry
Database: PDB / ID: 5j4s
Titlealpha-chymotrypsin from bovine pancreas in complex with a modified Bowman-Birk inhibitor from soybean
Components
  • Bowman-Birk type proteinase inhibitor
  • Chymotrypsinogen A
KeywordsHYDROLASE / bifunctional protease inhibitor / serine protease
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Cysteine Protease (Bromelain) Inhibitor, subunit H / Cysteine Protease (Bromelain) Inhibitor, subunit H / Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Cysteine Protease (Bromelain) Inhibitor, subunit H / Cysteine Protease (Bromelain) Inhibitor, subunit H / Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / Ribbon / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chymotrypsinogen A / Bowman-Birk type proteinase inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
Glycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsJohansson, E. / Tornoee, C.W.
CitationJournal: Synlett / Year: 2017
Title: Divergent Protein Synthesis of Bowman-Birk Protease Inhibitors, their Hydrodynamic Behavior and Co-crystallization with alpha-Chymotrypsin
Authors: Tornoee, C.W. / Johansson, E. / Wahlund, P.-O.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jan 10, 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: Chymotrypsinogen A
B: Bowman-Birk type proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)33,5892
Polymers33,5892
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-15 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.745, 78.793, 48.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Chymotrypsinogen A


Mass: 25686.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA-ALDRICH catalogue id C4129 / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein Bowman-Birk type proteinase inhibitor / BBI


Mass: 7902.884 Da / Num. of mol.: 1 / Fragment: UNP residues 40-110 / Mutation: M27L,A22T,L42F,Y45I,A47P / Source method: obtained synthetically / Source: (synth.) Glycine max (soybean) / References: UniProt: P01055
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10mM nickel chloride, 0.1M Tris-HCl, pH8.5, 20% (w/v) PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.103→34.85 Å / Num. obs: 17085 / % possible obs: 98 % / Redundancy: 7.1 % / Biso Wilson estimate: 29.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1204 / Net I/σ(I): 13.92
Reflection shellResolution: 2.103→2.178 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.5758 / Mean I/σ(I) obs: 2.23 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J4Q

5j4q


Resolution: 2.103→34.85 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.38
RfactorNum. reflection% reflection
Rfree0.2411 1511 4.89 %
Rwork0.1903 --
obs0.1929 16680 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.103→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 0 206 2485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022337
X-RAY DIFFRACTIONf_angle_d0.6123192
X-RAY DIFFRACTIONf_dihedral_angle_d13.5811428
X-RAY DIFFRACTIONf_chiral_restr0.043369
X-RAY DIFFRACTIONf_plane_restr0.004407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1028-2.17070.36471130.26612435X-RAY DIFFRACTION88
2.1707-2.24820.25161350.23992618X-RAY DIFFRACTION95
2.2482-2.33830.24291500.22142677X-RAY DIFFRACTION97
2.3383-2.44460.25641350.21272656X-RAY DIFFRACTION97
2.4446-2.57350.27421520.20352711X-RAY DIFFRACTION98
2.5735-2.73470.28511430.20512663X-RAY DIFFRACTION98
2.7347-2.94570.25461220.19992735X-RAY DIFFRACTION99
2.9457-3.2420.24621500.19362719X-RAY DIFFRACTION99
3.242-3.71070.26621330.18452761X-RAY DIFFRACTION99
3.7107-4.67350.19441390.15922691X-RAY DIFFRACTION99
4.6735-35.94860.20271390.17062716X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -15.0737 Å / Origin y: 13.7957 Å / Origin z: -7.1157 Å
111213212223313233
T0.1942 Å20.0127 Å2-0.0123 Å2-0.184 Å2-0.0042 Å2--0.2014 Å2
L0.4486 °20.0069 °2-0.1191 °2-0.2024 °2-0.1144 °2--0.5099 °2
S-0.0015 Å °-0.0168 Å °-0.0294 Å °0.0136 Å °-0.0312 Å °0.0256 Å °-0.0105 Å °0.0495 Å °0.0198 Å °
Refinement TLS groupSelection details: all

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