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- PDB-4kpg: Crystal structure of MycP1 from the ESX-1 type VII secretion system -

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Basic information

Entry
Database: PDB / ID: 4kpg
TitleCrystal structure of MycP1 from the ESX-1 type VII secretion system
ComponentsMembrane-anchored mycosin mycp1
KeywordsHYDROLASE / subtilisin / protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / plasma membrane
Similarity search - Function
Type VII secretion system peptidase S8A, mycosin / Peptidase S8/S53 domain / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.148 Å
AuthorsSolomonson, M. / Wasney, G.A. / Watanabe, N. / Gruninger, R.J. / Prehna, G. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure of the Mycosin-1 Protease from the Mycobacterial ESX-1 Protein Type VII Secretion System.
Authors: Solomonson, M. / Huesgen, P.F. / Wasney, G.A. / Watanabe, N. / Gruninger, R.J. / Prehna, G. / Overall, C.M. / Strynadka, N.C.
History
DepositionMay 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-anchored mycosin mycp1


Theoretical massNumber of molelcules
Total (without water)42,1541
Polymers42,1541
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.000, 94.080, 119.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

#1: Protein Membrane-anchored mycosin mycp1 / Peptidase S8 and S53 / subtilisin / kexin / sedolisin


Mass: 42153.746 Da / Num. of mol.: 1 / Fragment: UNP residues 24-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0083, MSMEI_0081 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QNL1, subtilisin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NaF, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97895 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 15, 2011
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.148→59.93 Å / Num. obs: 25383 / % possible obs: 99.82 %

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.148→47.04 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8852 / SU ML: 0.52 / σ(F): 0 / Phase error: 18.23 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1967 1281 5.08 %
Rwork0.166 --
obs0.1676 25226 99.7 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.466 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 125.02 Å2 / Biso mean: 35.9978 Å2 / Biso min: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.6739 Å2-0 Å20 Å2
2---8.8978 Å2-0 Å2
3---1.224 Å2
Refinement stepCycle: LAST / Resolution: 2.148→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 0 179 2943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072843
X-RAY DIFFRACTIONf_angle_d1.0493906
X-RAY DIFFRACTIONf_chiral_restr0.075441
X-RAY DIFFRACTIONf_plane_restr0.005538
X-RAY DIFFRACTIONf_dihedral_angle_d13.411021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1481-2.23410.27031250.20632611273699
2.2341-2.33570.24471560.194726232779100
2.3357-2.45890.22651550.180926262781100
2.4589-2.61290.22431410.168426472788100
2.6129-2.81460.19831310.162226352766100
2.8146-3.09780.21271510.158426552806100
3.0978-3.5460.18151530.163426562809100
3.546-4.4670.17941270.149227102837100
4.467-47.05130.17321420.16912782292499
Refinement TLS params.Method: refined / Origin x: 19.2387 Å / Origin y: 37.3645 Å / Origin z: 39.3087 Å
111213212223313233
T0.1982 Å20.0148 Å20.0321 Å2-0.1993 Å2-0.0752 Å2--0.2127 Å2
L1.2001 °2-0.3866 °2-0.1557 °2-1.1767 °20.1466 °2--1.0683 °2
S0.0354 Å °0.0395 Å °-0.018 Å °-0.1406 Å °0.1155 Å °-0.2818 Å °0.1884 Å °0.1356 Å °-0.069 Å °
Refinement TLS groupSelection details: (chain A and resid 23:402)

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