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- PDB-5j4q: alpha-chymotrypsin from bovine pancreas in complex with Bowman-Bi... -

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Basic information

Entry
Database: PDB / ID: 5j4q
Titlealpha-chymotrypsin from bovine pancreas in complex with Bowman-Birk inhibitor from soybean
Components
  • Bowman-Birk type proteinase inhibitor
  • Chymotrypsinogen A
KeywordsHYDROLASE / protease inhibitor / 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 / 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 / Mainly Beta
Similarity search - Domain/homology
Chymotrypsinogen A / Bowman-Birk type proteinase inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Glycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.303 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chymotrypsinogen A
B: Bowman-Birk type proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)33,5672
Polymers33,5672
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-13 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.163, 79.280, 51.529
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: Purchased from SIGMA-ALDRICH catalogue number C4129
Source: (natural) Bos taurus (domestic cattle) / Organ: pancreas / References: UniProt: P00766, chymotrypsin
#2: Protein Bowman-Birk type proteinase inhibitor / BBI


Mass: 7880.859 Da / Num. of mol.: 1 / Fragment: UNP residues 40-110 / Source method: isolated from a natural source / Details: SIGMA-ALDRICH catalogue id T9777 / Source: (natural) Glycine max (soybean) / References: UniProt: P01055
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 12%(w/v) PEG 20000, 0.1M MES, pH6.5

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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: Mar 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.303→28.568 Å / Num. obs: 14141 / % possible obs: 98 % / Redundancy: 4.1 % / Biso Wilson estimate: 43.76 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.0987 / Net I/σ(I): 12.9
Reflection shellResolution: 2.303→2.386 Å / Redundancy: 4 % / Rmerge(I) obs: 0.7356 / Mean I/σ(I) obs: 1.82 / % possible all: 100

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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: 1GL0,1K9B

1gl0

1k9b


Resolution: 2.303→28.568 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.46
RfactorNum. reflection% reflection
Rfree0.2673 1255 4.89 %
Rwork0.2102 --
obs0.2129 14123 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.61 Å2
Refinement stepCycle: LAST / Resolution: 2.303→28.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 0 78 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092309
X-RAY DIFFRACTIONf_angle_d1.1743152
X-RAY DIFFRACTIONf_dihedral_angle_d15.1971409
X-RAY DIFFRACTIONf_chiral_restr0.06364
X-RAY DIFFRACTIONf_plane_restr0.007400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3026-2.39480.35631520.28082691X-RAY DIFFRACTION96
2.3948-2.50370.35741330.28272719X-RAY DIFFRACTION96
2.5037-2.63560.36121460.26562761X-RAY DIFFRACTION97
2.6356-2.80060.28511320.25652714X-RAY DIFFRACTION97
2.8006-3.01660.38831480.26182740X-RAY DIFFRACTION97
3.0166-3.31980.27521270.23482729X-RAY DIFFRACTION97
3.3198-3.79920.29141500.20752720X-RAY DIFFRACTION96
3.7992-4.7830.19851370.17592683X-RAY DIFFRACTION95
4.783-28.57040.20861300.16542645X-RAY DIFFRACTION93

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