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- PDB-6pak: Insight into subtilisin E-S7 cleavage pattern based on crystal st... -

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Basic information

Entry
Database: PDB / ID: 6pak
TitleInsight into subtilisin E-S7 cleavage pattern based on crystal structure and hydrolysates peptide analysis
ComponentsSubtilisin E
KeywordsHYDROLASE / subtilisin
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / 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 ...Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 Å
AuthorsTang, H. / Shi, K. / Aihara, H.
Funding support United States, China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Natural Science Foundation of China (NSFC)31470160 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Enhancing subtilisin thermostability through a modified normalized B-factor analysis and loop-grafting strategy.
Authors: Tang, H. / Shi, K. / Shi, C. / Aihara, H. / Zhang, J. / Du, G.
History
DepositionJun 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Subtilisin E
B: Subtilisin E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6018
Polymers58,2722
Non-polymers3286
Water8,179454
1
A: Subtilisin E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3004
Polymers29,1361
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Subtilisin E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3004
Polymers29,1361
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.247, 80.475, 86.920
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 E


Mass: 29136.164 Da / Num. of mol.: 2 / Mutation: T236S,S264Q,S265H,G266P,S267K,T268E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: aprE, apr, aprA, sprE, BSU10300 / Production host: Escherichia coli (E. coli) / References: UniProt: P04189, subtilisin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, PEG 4,000, Tris-HCl (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→80.28 Å / Num. obs: 36622 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.214 / Net I/σ(I): 6.3
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.338 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2553 / CC1/2: 0.501 / Rsym value: 1.338 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3219: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6O44

6o44


Resolution: 1.98→46.216 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.46
RfactorNum. reflection% reflection
Rfree0.2864 1789 4.91 %
Rwork0.2394 --
obs0.2417 36465 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→46.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 0 20 455 4423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044042
X-RAY DIFFRACTIONf_angle_d0.6845512
X-RAY DIFFRACTIONf_dihedral_angle_d10.0422362
X-RAY DIFFRACTIONf_chiral_restr0.049634
X-RAY DIFFRACTIONf_plane_restr0.004722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.03360.33391480.31932623X-RAY DIFFRACTION98
2.0336-2.09340.35431420.30662584X-RAY DIFFRACTION99
2.0934-2.1610.30361220.28372673X-RAY DIFFRACTION99
2.161-2.23820.32151430.27932651X-RAY DIFFRACTION99
2.2382-2.32780.34731260.27142629X-RAY DIFFRACTION98
2.3278-2.43370.29681180.26372654X-RAY DIFFRACTION99
2.4337-2.5620.29261260.24892670X-RAY DIFFRACTION99
2.562-2.72250.2591230.23762671X-RAY DIFFRACTION99
2.7225-2.93270.28031480.2262666X-RAY DIFFRACTION99
2.9327-3.22780.26391740.22242638X-RAY DIFFRACTION98
3.2278-3.69470.26171340.20772696X-RAY DIFFRACTION99
3.6947-4.65420.25871170.18962728X-RAY DIFFRACTION98
4.6542-46.2290.29691680.25882793X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2594-0.94640.0882.8971-0.012.04010.1598-0.0057-0.1615-0.209-0.05820.0110.1585-0.1508-0.04380.1991-0.0350.02020.19940.01230.11781.9293-6.152-35.328
20.5878-1.1035-1.10962.47421.07352.60190.00770.0297-0.07950.06520.0979-0.2562-0.2473-0.1286-0.00250.2326-0.0105-0.00130.1370.00240.19136.106610.9126-21.4895
31.3037-0.1663-0.53431.5185-0.38341.259-0.1073-0.16540.08890.25890.09040.0783-0.0452-0.03290.03360.18990.01240.01060.17640.00630.18312.76763.0015-17.1163
43.5751-3.73041.89845.3594-0.95432.4442-0.2509-0.2822-0.06660.33220.2124-0.2826-0.0640.00690.08260.17930.0060.01740.14090.06620.155210.3023-10.002-12.0844
50.8894-0.0750.22971.1154-0.34380.6361-0.0164-0.0107-0.0808-0.02850.0095-0.0195-0.0048-0.0361-0.03420.14160.00170.0130.17250.00710.17225.4768-8.985-21.0747
64.94-2.81364.05633.8353-2.64216.25360.1451-0.1798-0.6601-0.15280.19290.19020.3636-0.2328-0.31910.1738-0.04390.00340.13460.02380.24013.1799-19.2447-23.8711
70.7720.4070.11981.48680.02730.6836-0.1057-0.2398-0.15130.20330.0731-0.1591-0.13510.14090.00350.2387-0.01620.02210.23280.02220.1726-35.2337-6.721-8.2469
80.543-0.46360.57411.6598-0.28741.9130.0518-0.0416-0.4082-0.04540.06190.07650.12960.03160.04720.20030.001-0.0020.17530.03690.2006-31.8507-20.8595-18.1005
91.12950.74931.13933.3511.36282.622-0.0761-0.0492-0.3410.11680.1687-0.2846-0.07170.3155-0.18650.27780.04110.06090.1728-0.05890.3884-30.5113-26.1987-25.6842
101.4490.02090.54051.54210.0321.8073-0.00330.055-0.153-0.2666-0.0279-0.02780.09060.01680.05670.22050.01140.03320.13540.00130.2098-32.4787-17.8078-23.0233
111.468-0.07050.35561.6702-0.1221.84820.01050.20470.0299-0.24260.0376-0.10930.17920.23840.09120.2217-0.00440.00110.2483-0.00690.191-38.2354-11.6329-33.3024
124.47340.07310.23652.03150.42281.7202-0.41350.5670.0368-0.48310.1887-0.3240.17150.19170.26420.16940.01440.02580.26810.01430.2038-26.8767-2.6284-31.4055
133.1643-0.67070.89610.44020.41931.6384-0.06720.63810.038-0.50720.2518-0.1241-0.10030.46350.04380.3143-0.027-0.00440.3354-0.04880.2756-31.852-2.5506-35.7446
141.8358-0.03070.01440.702-0.17781.0907-0.026-0.04230.0673-0.0345-0.0215-0.0302-0.04510.13320.03640.1826-0.00660.01310.1392-0.00830.1824-31.6294-3.9625-20.2199
155.65622.5849-3.02354.3451-2.43415.84360.23150.15940.8893-0.01340.08080.0379-0.4828-0.0525-0.39040.23220.0189-0.00460.12270.03090.2754-33.91156.4983-19.5693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 144 )
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 253 )
6X-RAY DIFFRACTION6chain 'A' and (resid 254 through 277 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 26 )
8X-RAY DIFFRACTION8chain 'B' and (resid 27 through 43 )
9X-RAY DIFFRACTION9chain 'B' and (resid 44 through 63 )
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 116 )
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 144 )
12X-RAY DIFFRACTION12chain 'B' and (resid 145 through 162 )
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 175 )
14X-RAY DIFFRACTION14chain 'B' and (resid 176 through 253 )
15X-RAY DIFFRACTION15chain 'B' and (resid 254 through 277 )

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