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- PDB-1y3b: Crystal structure of the complex of subtilisin BPN' with chymotry... -

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Basic information

Entry
Database: PDB / ID: 1y3b
TitleCrystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 E60S mutant
Components
  • chymotrypsin inhibitor 2
  • subtilisin BPN'
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine protease / inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / serine-type endopeptidase inhibitor activity / response to wounding / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / : / Fervidolysin N-terminal prodomain / Trypsin Inhibitor V; Chain A / Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily ...Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / : / Fervidolysin N-terminal prodomain / Trypsin Inhibitor V; Chain A / Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Subtilisin BPN' / Chymotrypsin inhibitor 2
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
Hordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRadisky, E.S. / Lu, C.J. / Kwan, G. / Koshland Jr., D.E.
CitationJournal: Biochemistry / Year: 2005
Title: Role of the intramolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2
Authors: Radisky, E.S. / Lu, C.J. / Kwan, G. / Koshland Jr., D.E.
History
DepositionNov 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: subtilisin BPN'
I: chymotrypsin inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,85210
Polymers35,6232
Non-polymers5,2298
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-25 kcal/mol
Surface area13220 Å2
MethodPISA
2
E: subtilisin BPN'
I: chymotrypsin inhibitor 2
hetero molecules

E: subtilisin BPN'
I: chymotrypsin inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,70420
Polymers71,2464
Non-polymers10,45816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_775-y+2,-x+2,-z+1/61
Buried area5690 Å2
ΔGint-48 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.253, 94.253, 186.135
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522

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Components

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Protein , 2 types, 2 molecules EI

#1: Protein subtilisin BPN' / E.C.3.4.21.62 / Subtilisin Novo / Subtilisin DFE / Alkaline protease


Mass: 28381.396 Da / Num. of mol.: 1 / Mutation: C-terminal 6-His tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: apr / Plasmid: pSer25 / Production host: Bacillus subtilis (bacteria) / Strain (production host): BG2036 / References: UniProt: P00782, subtilisin
#2: Protein chymotrypsin inhibitor 2


Mass: 7241.564 Da / Num. of mol.: 1 / Mutation: initiating Met, E60S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Plasmid: pCI2E60S / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q40059

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Non-polymers , 5 types, 512 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.7 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium citrate, isopropanol, PEG 4000, 4% acetone, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→81.65 Å / Num. all: 45872 / Num. obs: 43575 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Rsym value: 0.12 / Net I/σ(I): 15.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
EPMRphasing
REFMAC5.1.24refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TM3

1tm3


Resolution: 1.8→81.65 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.762 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17811 2280 5 %inherited from 1TM3
Rwork0.15055 ---
all0.15194 45855 --
obs0.15194 43575 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.009 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.16 Å20 Å2
2--0.33 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.8→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 83 504 3147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212689
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.963647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7955345
X-RAY DIFFRACTIONr_chiral_restr0.1350.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022014
X-RAY DIFFRACTIONr_nbd_refined0.2190.21317
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2364
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.370.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.245
X-RAY DIFFRACTIONr_mcbond_it0.9191.51715
X-RAY DIFFRACTIONr_mcangle_it1.53822772
X-RAY DIFFRACTIONr_scbond_it2.6783974
X-RAY DIFFRACTIONr_scangle_it4.4874.5874
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 165
Rwork0.225 3146

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