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- PDB-5ffn: Complex of subtilase SubTY from Bacillus sp. TY145 with chymotryp... -

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Basic information

Entry
Database: PDB / ID: 5ffn
TitleComplex of subtilase SubTY from Bacillus sp. TY145 with chymotrypsin inhibitor CI2A
Components
  • Enzyme subtilase SubTY from Bacillus sp. TY145
  • Subtilisin-chymotrypsin inhibitor-2A
KeywordsHYDROLASE / Protease / Subtilase / Complex / Inhibitor
Function / homology
Function and homology information


3.4.21.14 / serine-type endopeptidase inhibitor activity / response to wounding / serine-type endopeptidase activity / 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 / 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. ...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 / 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 / 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
Enzyme subtilase SubTY from Bacillus sp. TY145 / Subtilisin-chymotrypsin inhibitor-2A
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
Hordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMcAuley, K.E. / Svendsen, A. / Oestergaard, P.R. / Dohnalek, J. / Wilson, K.S.
CitationBook title: Understanding enzymes; Function, Design, Engineering and Analysis
Journal: Book / Year: 2016
Title: Stabilization of Enzymes by Metal Binding: Structures of Two Alkalophilic Bacillus Subtilases and Analysis of the Second Metal-Binding Site of the Subtilase Family
Authors: Dohnalek, J. / McAuley, K.E. / Brzozowski, A.M. / Oestergaard, P.R. / Svendsen, A. / Wilson, K.S.
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_abbrev / _database_2.pdbx_DOI ..._citation.journal_abbrev / _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
Revision 1.2Jan 10, 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
A: Enzyme subtilase SubTY from Bacillus sp. TY145
I: Subtilisin-chymotrypsin inhibitor-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0245
Polymers39,9212
Non-polymers1033
Water8,035446
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-48 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.753, 66.838, 107.082
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 Enzyme subtilase SubTY from Bacillus sp. TY145


Mass: 31814.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Bacillus sp. TY145, NCIMB 40339 / Source: (gene. exp.) Bacillus sp. (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A182DWC8*PLUS, 3.4.21.14
#2: Protein Subtilisin-chymotrypsin inhibitor-2A / CI-2A


Mass: 8106.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Production host: Escherichia coli (E. coli) / References: UniProt: P01053
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.6 Å3/Da / Density % sol: 53 % / Description: prism-shaped crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Complex was concentrated to 45 mg/ml in 10 mM Tris, pH 7.0. 1 microliter of protein solution with 1 microliter of a reservoir solution containing 5.5 M sodium formate, 0.2 M imidazole-malate ...Details: Complex was concentrated to 45 mg/ml in 10 mM Tris, pH 7.0. 1 microliter of protein solution with 1 microliter of a reservoir solution containing 5.5 M sodium formate, 0.2 M imidazole-malate pH 6.5, and 200 mM NDSB 201.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 1, 2001
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 40054 / Num. obs: 40054 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 17.676 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 33
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 5.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACK1.96.2data scaling
AMoREphasing
XTALVIEWmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVN

1svn


Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.004 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18839 2009 5 %RANDOM
Rwork0.15098 ---
obs0.15285 38044 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.614 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.81 Å20 Å2
3---0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 3 446 3202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222819
X-RAY DIFFRACTIONr_bond_other_d0.0010.022528
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9473835
X-RAY DIFFRACTIONr_angle_other_deg0.8835889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19224.867113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18515443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.021513
X-RAY DIFFRACTIONr_chiral_restr0.0950.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02536
X-RAY DIFFRACTIONr_nbd_refined0.2110.2584
X-RAY DIFFRACTIONr_nbd_other0.190.22635
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21398
X-RAY DIFFRACTIONr_nbtor_other0.0860.21569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2359
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.217
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1650.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8771.51847
X-RAY DIFFRACTIONr_mcbond_other0.281.5787
X-RAY DIFFRACTIONr_mcangle_it1.46322958
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.36131009
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.614.5877
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.796→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 138 -
Rwork0.194 2737 -
obs--99.34 %

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