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- PDB-7xr8: Structure of the S8 family protease A4095 -

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Basic information

Entry
Database: PDB / ID: 7xr8
TitleStructure of the S8 family protease A4095
ComponentsMajor intracellular serine protease
KeywordsHYDROLASE / S8 collagenolytic protease / bovine bone collagen / collagen oligopeptides / collagen peptide preparation / antioxidative activity
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Subtilisin Carlsberg-like catalytic 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily ...Subtilisin Carlsberg-like catalytic 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Major intracellular serine protease
Similarity search - Component
Biological speciesAnoxybacillus caldiproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsCheng, J.H. / Cao, H.Y. / Wang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structure of the S8 family protease A4095
Authors: Cheng, J.H. / Cao, H.Y. / Wang, P.
History
DepositionMay 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
A: Major intracellular serine protease
B: Major intracellular serine protease
C: Major intracellular serine protease
D: Major intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)142,1604
Polymers142,1604
Non-polymers00
Water11,566642
1
A: Major intracellular serine protease
B: Major intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)71,0802
Polymers71,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-15 kcal/mol
Surface area20830 Å2
MethodPISA
2
C: Major intracellular serine protease

D: Major intracellular serine protease


Theoretical massNumber of molelcules
Total (without water)71,0802
Polymers71,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area2460 Å2
ΔGint-16 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.617, 76.657, 84.314
Angle α, β, γ (deg.)90.000, 96.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Major intracellular serine protease


Mass: 35540.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anoxybacillus caldiproteolyticus (bacteria)
Gene: HNR31_003402 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A7V9Z9R1, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 642 / 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: 1.8 Å3/Da / Density % sol: 31.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium thiocyanate, 0.1 M Bis-Tris propane (pH 6.5), and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.94→39.53 Å / Num. obs: 73208 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 0.961 / CC star: 0.99 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.078 / Rrim(I) all: 0.141 / Net I/σ(I): 15.9
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6344 / CC1/2: 0.712 / CC star: 0.912 / Rpim(I) all: 0.285 / Rrim(I) all: 0.498 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F9M

6f9m


Resolution: 1.94→39.53 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 3600 4.92 %
Rwork0.1779 69540 -
obs0.1801 73140 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.28 Å2 / Biso mean: 28.8641 Å2 / Biso min: 13.81 Å2
Refinement stepCycle: final / Resolution: 1.94→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8677 0 0 642 9319
Biso mean---35.86 -
Num. residues----1151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-1.970.2581860.19961685177162
1.97-1.990.21041220.194326922814100
1.99-2.020.2971660.198826772843100
2.02-2.050.24361260.195527332859100
2.05-2.080.28531200.194227232843100
2.08-2.120.25491360.186527052841100
2.12-2.160.21771290.178927582887100
2.16-2.190.1991450.176126592804100
2.19-2.240.23111450.178726882833100
2.24-2.280.22711410.19327262867100
2.28-2.330.28281190.193727382857100
2.33-2.390.25951360.197926662802100
2.39-2.450.2781400.193927132853100
2.45-2.510.28481380.192727362874100
2.51-2.590.25311470.196727012848100
2.59-2.670.24111630.19292675283899
2.67-2.760.2451240.193727512875100
2.76-2.880.241410.200326742815100
2.88-3.010.24251470.198727462893100
3.01-3.160.27071300.184327242854100
3.16-3.360.20061580.18322695285399
3.36-3.620.18721280.163927362864100
3.62-3.990.20351990.14726742873100
3.99-4.560.16041300.141427562886100
4.56-5.740.18591410.159327602901100
5.75-39.530.21861430.19292749289297

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