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- PDB-1lw6: Crystal Structure of the Complex of Subtilisin BPN' with Chymotry... -

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Basic information

Entry
Database: PDB / ID: 1lw6
TitleCrystal Structure of the Complex of Subtilisin BPN' with Chymotrypsin Inhibitor 2 at 1.5 Angstrom Resolution
Components
  • SUBTILISIN BPN'
  • SUBTILISIN-CHYMOTRYPSIN INHIBITOR-2A
KeywordsHYDROLASE / SERINE PROTEASE / INHIBITOR
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. / Trypsin Inhibitor V; Chain A / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 ...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. / Trypsin Inhibitor V; Chain A / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / 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
Subtilisin BPN' / Subtilisin-chymotrypsin inhibitor-2A
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
Hordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRadisky, E.S. / Koshland JR., D.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: A clogged gutter mechanism for protease inhibitors.
Authors: Radisky, E.S. / Koshland Jr., D.E.
History
DepositionMay 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.5Oct 27, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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 1.6Feb 14, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
E: SUBTILISIN BPN'
I: SUBTILISIN-CHYMOTRYPSIN INHIBITOR-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0617
Polymers35,6372
Non-polymers4245
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-58 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.332, 56.597, 118.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SUBTILISIN BPN' / Subtilisin Novo / Alkaline protease


Mass: 28381.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: pser25 / Production host: Bacillus subtilis (bacteria) / Strain (production host): BG2036 / References: UniProt: P00782, subtilisin
#2: Protein SUBTILISIN-CHYMOTRYPSIN INHIBITOR-2A / CI-2A


Mass: 7255.586 Da / Num. of mol.: 1 / Mutation: E45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Strain: HIPROLY / Plasmid: pCI2ER1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01053
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, ammonium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mM1droppH5.8NaOAc
26.5 mg/mlprotein1drop
30.2 Mammonium sulfate1reservoir
40.1 Msodium cacodylate1reservoirpH6.5
530 %PEG80001reservoir

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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: Jul 21, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→29.66 Å / Num. all: 57529 / Num. obs: 57374 / % possible obs: 96.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.072 / Net I/σ(I): 15.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 7527 / Rsym value: 0.34 / % possible all: 88.9
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 29.7 Å / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 88.9 % / Rmerge(I) obs: 0.34

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Processing

Software
NameVersionClassification
REFMACrefinement
CNSrefinement
MOSFLMdata reduction
CCP4(SCALAdata scaling
TRUNCATEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2SNI

2sni


Resolution: 1.5→29.66 Å / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2889 5 %random
Rwork0.169 ---
all0.17 57529 --
obs0.17 57374 96.8 %-
Displacement parametersBiso mean: 12.71 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 21 505 3049
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.4
X-RAY DIFFRACTIONr_bond_refined_d0.007
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 29.7 Å / Rfactor all: 0.17 / Rfactor Rfree: 0.188 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.4

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