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- PDB-4kb5: Crystal structure of MycP1 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 4kb5
TitleCrystal structure of MycP1 from Mycobacterium smegmatis
ComponentsMembrane-anchored mycosin mycp1
KeywordsHYDROLASE / subtilisin-like serine protease / subtilase family / catalytic triad / autoinhibition / Serine protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / protein processing / serine-type endopeptidase activity / plasma membrane
Similarity search - Function
Type VII secretion system peptidase S8A, mycosin / Peptidase S8/S53 domain / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / 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: 2.15 Å
AuthorsSun, D.M. / He, Y. / Tian, C.L.
CitationJournal: Protein Cell / Year: 2013
Title: The putative propeptide of MycP1 in mycobacterial type VII secretion system does not inhibit protease activity but improves protein stability.
Authors: Sun, D. / Liu, Q. / He, Y. / Wang, C. / Wu, F. / Tian, C. / Zang, J.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-anchored mycosin mycp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,42311
Polymers42,5021
Non-polymers92110
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Membrane-anchored mycosin mycp1
hetero molecules

A: Membrane-anchored mycosin mycp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,84622
Polymers85,0042
Non-polymers1,84220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7230 Å2
ΔGint-18 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.114, 85.114, 193.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 42502.203 Da / Num. of mol.: 1 / Fragment: UNP residues 24-422
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) / Strain (production host): BL21(DE3) / References: UniProt: A0QNL1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 4.12 Å3/Da / Density % sol: 70.11 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.6 M Magnesium sulfate, 0.1 M MES pH 5.5 with a protein concentration of 20 mg ml-1, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97914 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.15→77.89 Å / Num. all: 39312 / Num. obs: 39312 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 25.9
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1947 / Rsym value: 0.507 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.691 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 1971 5 %RANDOM
Rwork0.18822 ---
obs0.18955 37215 99.29 %-
all-39312 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å2-0 Å20 Å2
2--0.92 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2807 0 60 177 3044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022914
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.9773984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3675386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59424.821112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6715388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9621516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222264
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 113 -
Rwork0.25 2364 -
obs-1947 94.83 %

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