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- PDB-4nsy: Wild-type lysobacter enzymogenes lysc endoproteinase covalently i... -

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Basic information

Entry
Database: PDB / ID: 4nsy
TitleWild-type lysobacter enzymogenes lysc endoproteinase covalently inhibited by TLCK
ComponentsLysyl endopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / ENDOPROTEINASE / AROMATIC STACK / ATOMIC RESOLUTION / SERINE PROTEASE / CATALYTIC TRIAD / COVALENT INHIBITION / TLCK / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


lysyl endopeptidase / serine-type peptidase activity / proteolysis / extracellular region
Similarity search - Function
Trypsin-like peptidase domain / 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
N-[(2S,3S)-7-AMINO-1-CHLORO-2-HYDROXYHEPTAN-3-YL]-4-METHYLBENZENESULFONAMIDE (BOUND FORM) / Chem-2OY / Lysyl endopeptidase
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsAsztalos, P. / Muller, A. / Holke, W. / Sobek, H. / Rudolph, M.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Atomic resolution structure of a lysine-specific endoproteinase from Lysobacter enzymogenes suggests a hydroxyl group bound to the oxyanion hole.
Authors: Asztalos, P. / Muller, A. / Holke, W. / Sobek, H. / Rudolph, M.G.
History
DepositionNov 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_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_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.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysyl endopeptidase
B: Lysyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2638
Polymers57,4422
Non-polymers8216
Water17,366964
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-29 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.579, 135.810, 45.587
Angle α, β, γ (deg.)90.00, 97.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysyl endopeptidase / Lys-C


Mass: 28721.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7M135, lysyl endopeptidase
#2: Chemical ChemComp-2OY / N-[(2S,3S)-7-amino-1-chloro-2-hydroxyheptan-3-yl]-4-methylbenzenesulfonamide (Bound Form) / Tosyllysine Chloromethyl Ketone (Bound Form)


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 334.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H23ClN2O3S
References: N-[(2S,3S)-7-AMINO-1-CHLORO-2-HYDROXYHEPTAN-3-YL]-4-METHYLBENZENESULFONAMIDE (BOUND FORM)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M CaCl2, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
211
ReflectionResolution: 1.1→37.6 Å / Num. obs: 182416 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.10728 / Net I/σ(I): 6.2978
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.95205 / Mean I/σ(I) obs: 1.0009 / % possible all: 83.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1520)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ARB

1arb


Resolution: 1.1→33.993 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 8425 5.02 %random
Rwork0.164 ---
obs0.1662 182401 94.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→33.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 44 964 4878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074091
X-RAY DIFFRACTIONf_angle_d1.1985580
X-RAY DIFFRACTIONf_dihedral_angle_d13.2821411
X-RAY DIFFRACTIONf_chiral_restr0.07606
X-RAY DIFFRACTIONf_plane_restr0.006734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11250.36592530.33094780X-RAY DIFFRACTION79
1.1125-1.12560.33552640.29835144X-RAY DIFFRACTION84
1.1256-1.13930.3243080.29095320X-RAY DIFFRACTION87
1.1393-1.15370.32072680.2845383X-RAY DIFFRACTION89
1.1537-1.16890.30833120.26845430X-RAY DIFFRACTION89
1.1689-1.18490.31932720.24375438X-RAY DIFFRACTION90
1.1849-1.20190.27792750.24145571X-RAY DIFFRACTION90
1.2019-1.21980.2682940.23695507X-RAY DIFFRACTION92
1.2198-1.23890.28563000.22725601X-RAY DIFFRACTION92
1.2389-1.25920.27662950.21455705X-RAY DIFFRACTION94
1.2592-1.28090.26532730.20925719X-RAY DIFFRACTION93
1.2809-1.30420.25573050.19175764X-RAY DIFFRACTION95
1.3042-1.32930.23423140.19365795X-RAY DIFFRACTION95
1.3293-1.35640.25293040.18515885X-RAY DIFFRACTION97
1.3564-1.38590.21913110.1855905X-RAY DIFFRACTION97
1.3859-1.41810.25022790.17836003X-RAY DIFFRACTION97
1.4181-1.45360.20263110.15735934X-RAY DIFFRACTION98
1.4536-1.49290.20532990.14565956X-RAY DIFFRACTION98
1.4929-1.53680.19432920.14275984X-RAY DIFFRACTION98
1.5368-1.58640.20093360.13946024X-RAY DIFFRACTION99
1.5864-1.64310.17493260.13936018X-RAY DIFFRACTION99
1.6431-1.70890.19453060.14266037X-RAY DIFFRACTION99
1.7089-1.78670.1883370.13886026X-RAY DIFFRACTION99
1.7867-1.88090.16923310.13726060X-RAY DIFFRACTION99
1.8809-1.99870.18963530.13836006X-RAY DIFFRACTION99
1.9987-2.1530.17753060.1386063X-RAY DIFFRACTION99
2.153-2.36960.18233290.14176045X-RAY DIFFRACTION99
2.3696-2.71240.19743400.14346032X-RAY DIFFRACTION99
2.7124-3.41680.19023200.14766030X-RAY DIFFRACTION99
3.4168-34.00950.17593350.14916088X-RAY DIFFRACTION99

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