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- PDB-6qoy: Crystal structure of L1 protease Lysobacter sp. XL1 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6qoy
TitleCrystal structure of L1 protease Lysobacter sp. XL1 in complex with AEBSF
ComponentsLytic endopeptidase preproenzyme
KeywordsHYDROLASE / Bacteriolytic protease L1 / Lysobacter sp. XL1 / Crystals / AEBSF
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold ...Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / 4-(2-azanylethyl)benzenesulfonic acid / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Lytic endopeptidase preproenzyme
Similarity search - Component
Biological speciesLysobacter sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGabdulkhakov, A. / Tishchenko, S. / Kudryakova, I. / Afoshin, A. / Vasilyeva, N.
CitationJournal: Process Biochem / Year: 2019
Title: Serine bacteriolytic protease L1 of Lysobacter sp. XL1 complexed with protease inhibitor AEBSF: features of interaction
Authors: Kudryakova, I. / Gabdulkhakov, A. / Tishchenko, S. / Afoshin, A. / Vasilyeva, N.
History
DepositionFeb 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lytic endopeptidase preproenzyme
B: Lytic endopeptidase preproenzyme
C: Lytic endopeptidase preproenzyme
D: Lytic endopeptidase preproenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,57730
Polymers79,3924
Non-polymers3,18526
Water5,603311
1
A: Lytic endopeptidase preproenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6748
Polymers19,8481
Non-polymers8267
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lytic endopeptidase preproenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7849
Polymers19,8481
Non-polymers9368
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lytic endopeptidase preproenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5827
Polymers19,8481
Non-polymers7346
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lytic endopeptidase preproenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5376
Polymers19,8481
Non-polymers6895
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.855, 122.553, 78.988
Angle α, β, γ (deg.)90.00, 98.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Lytic endopeptidase preproenzyme


Mass: 19848.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter sp. (strain XL1) (bacteria) / Strain: XL1 / Gene: alpA / Plasmid: PAPROZ / Production host: Escherichia coli (E. coli) / References: UniProt: D2K8B3

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Non-polymers , 8 types, 337 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF


Mass: 203.234 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-JAT / 4-(2-azanylethyl)benzenesulfonic acid


Mass: 201.243 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H11NO3S
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1,4M Lithium sulphate, 0,1M BisTris,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 65564 / % possible obs: 99.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.13
Reflection shellResolution: 1.86→1.97 Å / Rmerge(I) obs: 0.8 / Num. unique all: 10356

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MRR

5mrr


Resolution: 1.9→48.207 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 26.51
RfactorNum. reflection% reflection
Rfree0.24 6124 5.08 %
Rwork0.1999 --
obs0.202 61461 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5560 0 193 311 6064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076028
X-RAY DIFFRACTIONf_angle_d0.8668178
X-RAY DIFFRACTIONf_dihedral_angle_d11.4664424
X-RAY DIFFRACTIONf_chiral_restr0.059894
X-RAY DIFFRACTIONf_plane_restr0.0051085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.36362050.31323736X-RAY DIFFRACTION99
1.9216-1.94420.38271930.32023821X-RAY DIFFRACTION99
1.9442-1.96790.32431840.31443837X-RAY DIFFRACTION98
1.9679-1.99280.35692000.31253889X-RAY DIFFRACTION98
1.9928-2.0190.31431610.28693625X-RAY DIFFRACTION95
2.019-2.04670.30962180.27933628X-RAY DIFFRACTION96
2.0467-2.07590.28371850.26083925X-RAY DIFFRACTION99
2.0759-2.10690.29312290.27213840X-RAY DIFFRACTION100
2.1069-2.13990.30781900.2623808X-RAY DIFFRACTION100
2.1399-2.17490.27262120.24753879X-RAY DIFFRACTION100
2.1749-2.21240.32192380.25583877X-RAY DIFFRACTION99
2.2124-2.25270.28312170.23653792X-RAY DIFFRACTION100
2.2527-2.2960.31862220.23713806X-RAY DIFFRACTION99
2.296-2.34290.27662070.23263885X-RAY DIFFRACTION99
2.3429-2.39380.25332150.21893791X-RAY DIFFRACTION98
2.3938-2.44950.2831860.23313739X-RAY DIFFRACTION96
2.4495-2.51070.29821980.22943686X-RAY DIFFRACTION97
2.5107-2.57860.30792190.22933868X-RAY DIFFRACTION100
2.5786-2.65450.31762020.21893853X-RAY DIFFRACTION100
2.6545-2.74020.25141990.20373838X-RAY DIFFRACTION100
2.7402-2.83810.24612280.19813820X-RAY DIFFRACTION99
2.8381-2.95170.22881750.20043941X-RAY DIFFRACTION99
2.9517-3.0860.28472320.20323787X-RAY DIFFRACTION99
3.086-3.24870.22461840.19673762X-RAY DIFFRACTION97
3.2487-3.45220.21371910.18333893X-RAY DIFFRACTION100
3.4522-3.71860.18622060.16233814X-RAY DIFFRACTION100
3.7186-4.09270.17622280.13833843X-RAY DIFFRACTION100
4.0927-4.68450.14272070.1193797X-RAY DIFFRACTION98
4.6845-5.90030.17452070.13973856X-RAY DIFFRACTION100
5.9003-48.22270.19391860.17573856X-RAY DIFFRACTION99

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