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- PDB-3cnq: Prosubtilisin Substrate Complex of Subtilisin SUBT_BACAM -

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Basic information

Entry
Database: PDB / ID: 3cnq
TitleProsubtilisin Substrate Complex of Subtilisin SUBT_BACAM
Components(Subtilisin BPN') x 2
KeywordsHYDROLASE / uncleaved / proenzyme / substrate complex / Metal-binding / Protease / Secreted / Serine protease / Sporulation / Zymogen
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase S8 propeptide/proteinase inhibitor I9 / 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 ...Peptidase S8 propeptide/proteinase inhibitor I9 / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å
AuthorsGallagher, D.T. / Bryan, P.N.
CitationJournal: Biochemistry / Year: 2008
Title: Engineering substrate preference in subtilisin: structural and kinetic analysis of a specificity mutant.
Authors: Ruan, B. / London, V. / Fisher, K.E. / Gallagher, D.T. / Bryan, P.N.
History
DepositionMar 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Subtilisin BPN'
S: Subtilisin BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5347
Polymers35,2072
Non-polymers3275
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-155.8 kcal/mol
Surface area12770 Å2
MethodPISA
2
P: Subtilisin BPN'

S: Subtilisin BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5347
Polymers35,2072
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-159.7 kcal/mol
Surface area14310 Å2
MethodPISA
3
P: Subtilisin BPN'

S: Subtilisin BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5347
Polymers35,2072
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation2_455-x-1/2,-y,z+1/21
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-159.8 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.195, 72.941, 93.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 8786.066 Da / Num. of mol.: 1 / Fragment: Prodomain
Mutation: K27E, V37L, Q40C, K57E, H72K, V73L, A74Y, H75R, Y77L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: apr / Plasmid: pG5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00782
#2: Protein Subtilisin BPN' / Subtilisin Novo / Subtilisin DFE / Alkaline protease


Mass: 26420.447 Da / Num. of mol.: 1 / Fragment: Enzyme domain
Mutation: Q2K, S3C, P5S, S9A, I31L, D32A, K43N, M50F, A73L, Y104A, G128S, E156S, G166S, G169A, S188P, Q206C, N212G, K217L, N218S, S221A, T254A, Q271E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: apr / Plasmid: pG5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00782, subtilisin
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THAT RESIDUES 17-23 TMSTMSA WAS REPLACED WITH GFKSC

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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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 18% PEG8K, 0.2 M Zn Acetate, 0.1 M Na Cacodylate, pH 6.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Date: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 5.5 % / Av σ(I) over netI: 17 / Number: 178892 / Rmerge(I) obs: 0.069 / Χ2: 2.33 / D res high: 1.71 Å / D res low: 50 Å / Num. obs: 32590 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.685098.710.042.7635.3
2.923.6899.910.0593.6225.6
2.552.9299.910.0753.1045.8
2.322.5510010.092.755.8
2.152.3299.910.1072.5615.7
2.032.1599.810.1342.175.7
1.932.0399.810.1691.8575.7
1.841.9399.810.2151.575.7
1.771.8499.910.2691.2545.3
1.711.7799.410.2931.1254.3
ReflectionResolution: 1.71→50 Å / Num. all: 32590 / Num. obs: 32590 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.069 / Χ2: 2.325 / Net I/σ(I): 17
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.293 / Num. unique all: 3202 / Χ2: 1.125 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.3 Å9.99 Å
Translation3.3 Å9.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→10 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.199 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1641 5.1 %RANDOM
Rwork0.191 ---
all0.199 32590 --
obs0.193 32338 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.86 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.71→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 5 259 2665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222429
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9583300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6285330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.35225.92681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64815378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.593153
X-RAY DIFFRACTIONr_chiral_restr0.1080.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021808
X-RAY DIFFRACTIONr_nbd_refined0.2260.21150
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21661
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2148
X-RAY DIFFRACTIONr_metal_ion_refined0.0420.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3270.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.29
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2750.22
X-RAY DIFFRACTIONr_mcbond_it1.0361.51676
X-RAY DIFFRACTIONr_mcangle_it1.68422615
X-RAY DIFFRACTIONr_scbond_it2.6593845
X-RAY DIFFRACTIONr_scangle_it3.8724.5685
LS refinement shellResolution: 1.71→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 145 -
Rwork0.218 2067 -
all-2212 -
obs--95.43 %

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