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- PDB-5mrr: Crystal structure of L1 protease of Lysobacter sp. XL1 -

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Basic information

Entry
Database: PDB / ID: 5mrr
TitleCrystal structure of L1 protease of Lysobacter sp. XL1
ComponentsLytic endopeptidase preproenzyme
KeywordsHYDROLASE / Bacteriolytic protease L1 / Lysobacter sp. XL1 / Crystals
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
Lytic endopeptidase preproenzyme
Similarity search - Component
Biological speciesLysobacter sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGabdulkhakov, A. / Tishchenko, S. / Lisov, A. / Leontievsky, A.
CitationJournal: To Be Published
Title: Crystal structure of L1 protease of Lysobacter sp. XL1
Authors: Gabdulkhakov, A. / Tishchenko, S. / Lisov, A. / Leontievsky, A.
History
DepositionDec 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)81,14830
Polymers79,3924
Non-polymers1,75626
Water11,007611
1
A: Lytic endopeptidase preproenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1787
Polymers19,8481
Non-polymers3306
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lytic endopeptidase preproenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4539
Polymers19,8481
Non-polymers6058
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lytic endopeptidase preproenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3878
Polymers19,8481
Non-polymers5397
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lytic endopeptidase preproenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1306
Polymers19,8481
Non-polymers2825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.710, 96.480, 118.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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) / Gene: alpA / Plasmid: pAproZ / Production host: Escherichia coli (E. coli) / References: UniProt: D2K8B3

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Non-polymers , 6 types, 637 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
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
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 199062 / % possible obs: 99.1 % / Redundancy: 4.98 % / Net I/σ(I): 8.9
Reflection shellResolution: 1.25→1.34 Å / Redundancy: 4.98 % / Mean I/σ(I) obs: 1.4 / % possible all: 98

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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: 2alp

2alp


Resolution: 1.35→19.985 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.97 / Phase error: 18.08
RfactorNum. reflection% reflection
Rfree0.1904 14854 4.89 %
Rwork0.157 --
obs0.1586 158793 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→19.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5560 0 92 611 6263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066017
X-RAY DIFFRACTIONf_angle_d0.8518198
X-RAY DIFFRACTIONf_dihedral_angle_d22.4852150
X-RAY DIFFRACTIONf_chiral_restr0.09903
X-RAY DIFFRACTIONf_plane_restr0.0051099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.3144960.2719502X-RAY DIFFRACTION97
1.3653-1.38140.30145280.26569386X-RAY DIFFRACTION96
1.3814-1.39820.29735320.26039463X-RAY DIFFRACTION97
1.3982-1.41590.29244700.24079527X-RAY DIFFRACTION97
1.4159-1.43460.26645340.22849442X-RAY DIFFRACTION97
1.4346-1.45420.25214650.21459613X-RAY DIFFRACTION97
1.4542-1.4750.24295030.21019533X-RAY DIFFRACTION97
1.475-1.4970.23345020.20329573X-RAY DIFFRACTION98
1.497-1.52040.2414490.20289703X-RAY DIFFRACTION98
1.5204-1.54530.25064430.19229637X-RAY DIFFRACTION98
1.5453-1.57190.2254850.17939639X-RAY DIFFRACTION98
1.5719-1.60050.21185040.16859714X-RAY DIFFRACTION99
1.6005-1.63130.21345040.16399679X-RAY DIFFRACTION99
1.6313-1.66450.2165030.16369591X-RAY DIFFRACTION98
1.6645-1.70070.21774750.16229502X-RAY DIFFRACTION96
1.7007-1.74030.20144910.15849701X-RAY DIFFRACTION99
1.7403-1.78380.20115010.14689681X-RAY DIFFRACTION99
1.7838-1.8320.18145020.14239786X-RAY DIFFRACTION100
1.832-1.88580.17484770.13259751X-RAY DIFFRACTION99
1.8858-1.94660.16884880.13349781X-RAY DIFFRACTION100
1.9466-2.01620.17785180.13429731X-RAY DIFFRACTION100
2.0162-2.09680.17894560.12579851X-RAY DIFFRACTION100
2.0968-2.19210.16325300.13219679X-RAY DIFFRACTION99
2.1921-2.30750.1744970.13569649X-RAY DIFFRACTION98
2.3075-2.45190.19554830.149475X-RAY DIFFRACTION97
2.4519-2.64080.1795420.15019693X-RAY DIFFRACTION100
2.6408-2.90580.1864790.15329797X-RAY DIFFRACTION100
2.9058-3.32460.16675510.1559717X-RAY DIFFRACTION100
3.3246-4.18230.15634570.14289674X-RAY DIFFRACTION99
4.1823-19.98730.15084890.14639619X-RAY DIFFRACTION98

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