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- PDB-4kg7: Structure of MycP3 protease from the type VII (ESX-3) secretion s... -

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Basic information

Entry
Database: PDB / ID: 4kg7
TitleStructure of MycP3 protease from the type VII (ESX-3) secretion system.
ComponentsPeptidase S8 and S53, subtilisin, kexin, sedolisin
KeywordsHYDROLASE / serine protease / subtilase / mycosin / protein secretion / subtilisin fold / ESX / type VII secretion system
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / plasma membrane
Similarity search - Function
Autotransporter serine protease peptidase domain / Type VII secretion system peptidase S8A, mycosin / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family ...Autotransporter serine protease peptidase domain / Type VII secretion system peptidase S8A, mycosin / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilase family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKorotkov, K.V. / Evans, T.J.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Understanding specificity of the mycosin proteases in ESX/type VII secretion by structural and functional analysis.
Authors: Wagner, J.M. / Evans, T.J. / Chen, J. / Zhu, H. / Houben, E.N. / Bitter, W. / Korotkov, K.V.
History
DepositionApr 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Sep 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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: Peptidase S8 and S53, subtilisin, kexin, sedolisin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5772
Polymers38,5421
Non-polymers351
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.820, 46.950, 47.540
Angle α, β, γ (deg.)77.270, 68.350, 74.470
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Peptidase S8 and S53, subtilisin, kexin, sedolisin / Subtilase family protein / MycP3 protease


Mass: 38541.852 Da / Num. of mol.: 1 / Fragment: residues 26-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_0624, MSMEI_0608, MycP3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0QQ47
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.2M MAGNESIUM CHLORIDE, 0.1M TRIS-HCL, 20% PEG8000, 0.01M NICKEL CHLORIDE, pH 8.4, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 52615 / Num. obs: 48069 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.151 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.540.4652.045675225257.9
1.54-1.580.3562.617110278473.1
1.58-1.630.3113.28986342292.7
1.63-1.680.2563.778952337994.5
1.68-1.730.2054.788750329094.9
1.73-1.790.1586.298510319694.9
1.79-1.860.1237.778213310095.3
1.86-1.940.09310.117914298195.9
1.94-2.020.07213.167554284795.9
2.02-2.120.05815.97327276796.2
2.12-2.240.04918.266949262796.3
2.24-2.370.04221.276588248296.7
2.37-2.540.03823.276193233396.8
2.54-2.740.03326.025716216996.9
2.74-30.02930.915321202297.2
3-3.360.02336.354752181797.3
3.36-3.880.0241.454268162997.7
3.88-4.750.01745.033564136497.9
4.75-6.710.01943.072748105198.7
6.710.01747.62145355794.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HVL

4hvl


Resolution: 1.5→43.82 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1771 / WRfactor Rwork: 0.1437 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9036 / SU B: 2.316 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0739 / SU Rfree: 0.0767 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1846 2432 5.1 %RANDOM
Rwork0.151 ---
obs0.1527 48069 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.76 Å2 / Biso mean: 15.6201 Å2 / Biso min: 4.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.03 Å2-0.07 Å2
2---0.12 Å2-0.1 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 1 533 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192712
X-RAY DIFFRACTIONr_bond_other_d0.0010.022541
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9683732
X-RAY DIFFRACTIONr_angle_other_deg0.8043.0015855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6155375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05224100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47915369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6491521
X-RAY DIFFRACTIONr_chiral_restr0.0850.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_mcbond_it0.7530.6951482
X-RAY DIFFRACTIONr_mcbond_other0.7530.6941481
X-RAY DIFFRACTIONr_mcangle_it1.3351.0361851
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 92 -
Rwork0.237 2155 -
all-2247 -
obs--57.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8180.1335-0.15760.8657-0.02840.39850.019-0.0460.04630.01080.00510.0382-0.0235-0.0229-0.02420.0265-0.0057-0.01210.031-0.01010.019623.98331.6574.959
20.65430.1340.06450.7295-0.08170.60680.007-0.0062-0.04170.01890.0004-0.07770.0270.0211-0.00740.0288-0.002-0.00890.0239-0.01080.031836.18224.7855.182
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 246
2X-RAY DIFFRACTION2A247 - 399

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