[English] 日本語
Yorodumi
- PDB-4kg7: Structure of MycP3 protease from the type VII (ESX-3) secretion s... -

+
Open data


ID or keywords:

Loading...

-
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


membrane => GO:0016020 / serine-type endopeptidase activity / 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 / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold ...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 / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more