[English] 日本語
Yorodumi
- PDB-4j94: Crystal structure of MycP1 from the ESX-1 type VII secretion system -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j94
TitleCrystal structure of MycP1 from the ESX-1 type VII secretion system
ComponentsMembrane-anchored mycosin mycp1
KeywordsHYDROLASE / Subtilisin-like / Protease / secretion system
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 / molecular replacement / Resolution: 1.857 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
DepositionFeb 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Membrane-anchored mycosin mycp1


Theoretical massNumber of molelcules
Total (without water)42,6181
Polymers42,6181
Non-polymers00
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.490, 77.290, 84.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 42618.309 Da / Num. of mol.: 1 / Fragment: 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.: 421 / 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: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.77
Details: 0.1M Bis-Tris propane 0.18 M sodium thiocyanate 26% PEG 3350, pH 6.77, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97895 Å
DetectorType: RAYONIX MX-300 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.581→47.04 Å / Num. obs: 27671 / % possible obs: 99.9 % / Redundancy: 5 % / Rsym value: 0.07 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.25-2.3750.2063.61587431770.206100
2.37-2.5250.1564.61501730110.156100
2.52-2.6950.1116.51423828500.111100
2.69-2.950.0917.41304326160.091100
2.9-3.1850.0788.31227424590.078100
3.18-3.5650.05311.71098722000.05399.9
3.56-4.1150.0658.6981519820.06599.9
4.11-5.034.90.078.2824716690.0799.8
5.03-7.124.90.04711.5637213020.04799.3
7.12-47.044.60.04213.534857610.04298.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASERphasing
PHENIXdev_1284refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.857→37.218 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8861 / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 1389 5.02 %RANDOM
Rwork0.1553 ---
all0.1571 27715 --
obs0.1571 27657 86.2 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.93 Å2 / Biso mean: 17.3995 Å2 / Biso min: 3.58 Å2
Refinement stepCycle: LAST / Resolution: 1.857→37.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 0 421 3139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062812
X-RAY DIFFRACTIONf_angle_d1.1063872
X-RAY DIFFRACTIONf_chiral_restr0.073440
X-RAY DIFFRACTIONf_plane_restr0.005533
X-RAY DIFFRACTIONf_dihedral_angle_d10.3771010
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.857-1.92340.27221170.22642175229282
1.9234-2.00040.21341130.16532126223973
2.0004-2.09140.22311260.15162373249978
2.0914-2.20160.18541560.147529793135100
2.2016-2.33960.20591250.14842325245077
2.3396-2.52020.18291580.152230213179100
2.5202-2.77370.1861360.15242556269284
2.7737-3.17490.16591610.155630593220100
3.1749-3.99930.1891260.14512429255578
3.9993-37.2250.17971710.153432253396100
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)
11.0011-0.6641-0.49811.09290.82531.41710.070.00090.0013-0.10190.0623-0.1136-0.0190.1651-0.16470.111-0.02230.02220.1546-0.02460.13663.75471.4375-5.3636
21.3679-0.20080.12961.11720.29780.91760.0410.10680.1483-0.125-0.13110.1992-0.0841-0.15880.07060.08590.0088-0.00940.1139-0.00660.1246-26.41723.8131-15.9477
31.89030.35240.54280.41770.11350.92660.0164-0.10040.03770.0286-0.03160.035-0.0228-0.0450.00510.0972-0.00960.0130.0728-0.0170.0698-14.4280.7999-3.8731
41.4599-0.04180.07150.93250.24111.06720.0236-0.02560.2583-0.01290.0849-0.1549-0.08310.1555-0.03450.07090.0010.0110.0928-0.02920.09737.53173.5057-6.0318
52.99581.8587-0.68512.9789-1.13181.37410.01620.10080.11570.03430.0667-0.0422-0.1160.0259-0.07790.1119-0.0023-0.00180.0522-0.01510.02831.99762.2916-14.2082
61.2933-0.3545-0.0261.476-0.98541.4237-0.02470.05540.05450.05120.005-0.03150.04250.07860.01360.0477-0.0045-0.01540.0667-0.02540.0461-0.7854-1.8343-15.8031
70.90170.47870.25161.23380.16150.8314-0.13760.5074-0.0037-0.25250.15-0.0289-0.20140.1703-0.01160.1186-0.05420.0050.16840.01860.0911-2.05366.6035-27.0808
81.1557-0.1306-0.2570.49580.21720.87530.0381-0.00220.06610.0104-0.01120.0017-0.0204-0.00870.00550.05350.0006-0.0030.04230.00550.0438-15.09981.7063-16.8905
91.61720.2836-0.07572.03780.05881.2595-0.0090.1119-0.0672-0.11960.0067-0.06150.09240.1228-0.01010.0783-0.0061-0.01210.10420.0040.0411-12.2583-5.1753-29.9299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 52 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 86 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 162 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 193 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 194 through 215 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 246 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 247 through 293 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 294 through 365 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 366 through 403 )A0

+
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://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