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- PDB-4m1z: Crystal structure of MycP1 with the N-terminal propeptide removed -

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Basic information

Entry
Database: PDB / ID: 4m1z
TitleCrystal structure of MycP1 with the N-terminal propeptide removed
Components(Membrane-anchored mycosin mycp1) x 2
KeywordsHYDROLASE / subtilisin-like / propeptide-removed / serine protease / ESX-1 system / membrane-anchored
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 / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSun, D.M. / He, Y. / Wang, C.L. / Zang, J.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.M. / Liu, Q. / He, Y. / Wang, C.L. / Wu, F.M. / Tian, C.L. / Zang, J.Y.
History
DepositionAug 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-anchored mycosin mycp1
B: Membrane-anchored mycosin mycp1
C: Membrane-anchored mycosin mycp1
D: Membrane-anchored mycosin mycp1


Theoretical massNumber of molelcules
Total (without water)81,7154
Polymers81,7154
Non-polymers00
Water5,242291
1
A: Membrane-anchored mycosin mycp1
C: Membrane-anchored mycosin mycp1


Theoretical massNumber of molelcules
Total (without water)40,8582
Polymers40,8582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-10 kcal/mol
Surface area13370 Å2
MethodPISA
2
B: Membrane-anchored mycosin mycp1
D: Membrane-anchored mycosin mycp1


Theoretical massNumber of molelcules
Total (without water)40,8582
Polymers40,8582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-9 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.311, 83.611, 98.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 38626.934 Da / Num. of mol.: 2 / Fragment: UNP residues 63-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_0083, MSMEI_0081 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QNL1, subtilisin
#2: Protein/peptide Membrane-anchored mycosin mycp1 / Peptidase S8 and S53 / subtilisin / kexin / sedolisin


Mass: 2230.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_0083, MSMEI_0081 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QNL1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 63-402 IN THE CHAINS C AND D ARE DELETIONS.

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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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M sodium citrate, 20% (v/v) 2-propanol, 20% (w/v) PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97906 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 33595 / Num. obs: 33595 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 12.912
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.845 / Rsym value: 0.444 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KB5

4kb5


Resolution: 2.25→37.28 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.548 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.297 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22183 1519 5 %RANDOM
Rwork0.16598 ---
obs0.1688 28885 91.45 %-
all-33595 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.394 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4742 0 0 291 5033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194848
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9626656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34424.332187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10515650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7171531
X-RAY DIFFRACTIONr_chiral_restr0.0850.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223807
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 69 -
Rwork0.172 1240 -
obs--55.84 %

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