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- PDB-5mrt: Crystal structure of L5 protease Lysobacter sp. XL1 -

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Basic information

Entry
Database: PDB / ID: 5mrt
TitleCrystal structure of L5 protease Lysobacter sp. XL1
ComponentsLytic endopeptidase preproenzyme
KeywordsHYDROLASE / Bacteriolytic protease L5 / Lysobacter sp. XL1 / Crystals / AEBSF
Function / homology
Function and homology information


serine-type endopeptidase activity / extracellular region
Similarity search - Function
Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / 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
FORMIC ACID / Lytic endopeptidase preproenzyme
Similarity search - Component
Biological speciesLysobacter sp.
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGabdulkhakov, A. / Tishchenko, S. / Lisov, A. / Leontievsky, A.
CitationJournal: To Be Published
Title: Crystal structure of L5 protease 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,04612
Polymers41,5962
Non-polymers45010
Water7,368409
1
A: Lytic endopeptidase preproenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0287
Polymers20,7981
Non-polymers2306
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lytic endopeptidase preproenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0185
Polymers20,7981
Non-polymers2204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.549, 66.668, 96.642
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, 2 molecules AB

#1: Protein Lytic endopeptidase preproenzyme


Mass: 20798.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter sp. (strain XL1) (bacteria) / Gene: alpB / Production host: Escherichia coli (E. coli) / References: UniProt: D2K8B4

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Non-polymers , 5 types, 419 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2,7M Na formate, 0,2 M ammonium acetate, PIPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.6→35 Å / Num. obs: 53331 / % possible obs: 98.6 % / Redundancy: 5.9 % / Net I/σ(I): 9.7
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.46 % / Mean I/σ(I) obs: 1.8 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MRR

5mrr


Resolution: 1.6→33.334 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.49
RfactorNum. reflection% reflection
Rfree0.227 2547 4.8 %
Rwork0.1675 --
obs0.1704 53022 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→33.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 27 409 3197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062879
X-RAY DIFFRACTIONf_angle_d0.9113917
X-RAY DIFFRACTIONf_dihedral_angle_d19.88998
X-RAY DIFFRACTIONf_chiral_restr0.065457
X-RAY DIFFRACTIONf_plane_restr0.005511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63080.28721280.20332734X-RAY DIFFRACTION97
1.6308-1.66410.27771190.19472772X-RAY DIFFRACTION97
1.6641-1.70020.27431360.18622755X-RAY DIFFRACTION98
1.7002-1.73980.21381320.17472768X-RAY DIFFRACTION99
1.7398-1.78330.2561200.172817X-RAY DIFFRACTION99
1.7833-1.83150.24241300.1772812X-RAY DIFFRACTION99
1.8315-1.88540.27361260.17392799X-RAY DIFFRACTION99
1.8854-1.94630.25491380.17882825X-RAY DIFFRACTION99
1.9463-2.01580.24651520.16782822X-RAY DIFFRACTION99
2.0158-2.09650.22741570.16562804X-RAY DIFFRACTION99
2.0965-2.19190.22781440.16092791X-RAY DIFFRACTION99
2.1919-2.30740.21871540.17822808X-RAY DIFFRACTION98
2.3074-2.4520.26521470.19992769X-RAY DIFFRACTION97
2.452-2.64120.24821570.18922778X-RAY DIFFRACTION98
2.6412-2.90690.22871720.19232796X-RAY DIFFRACTION98
2.9069-3.32720.20721550.16462853X-RAY DIFFRACTION99
3.3272-4.19060.21711380.13022859X-RAY DIFFRACTION97
4.1906-33.34120.15731420.14022913X-RAY DIFFRACTION95

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