[English] 日本語
Yorodumi
- PDB-6sf7: Atomic resolution structure of SplF protease from Staphylococcus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sf7
TitleAtomic resolution structure of SplF protease from Staphylococcus aureus
ComponentsSerine protease SplF
KeywordsHYDROLASE / Virulence factor / protease / bacterial
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / extracellular region
Similarity search - Function
Serine proteases, V8 family, histidine active site / Serine proteases, V8 family, histidine active site. / Peptidase S1B / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Serine protease SplF
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGolik, P. / Stach, N. / Karim, A. / Dubin, G.
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural Determinants of Substrate Specificity of SplF Protease from Staphylococcus aureus .
Authors: Stach, N. / Karim, A. / Golik, P. / Kitel, R. / Pustelny, K. / Gruba, N. / Groborz, K. / Jankowska, U. / Kedracka-Krok, S. / Wladyka, B. / Drag, M. / Lesner, A. / Dubin, G.
History
DepositionAug 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine protease SplF
B: Serine protease SplF
C: Serine protease SplF
D: Serine protease SplF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,01423
Polymers88,1834
Non-polymers1,83119
Water8,107450
1
A: Serine protease SplF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5366
Polymers22,0461
Non-polymers4905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine protease SplF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5887
Polymers22,0461
Non-polymers5426
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine protease SplF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4605
Polymers22,0461
Non-polymers4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine protease SplF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4305
Polymers22,0461
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.000, 58.580, 62.300
Angle α, β, γ (deg.)104.570, 95.310, 90.600
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Serine protease SplF


Mass: 22045.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria)
Gene: splF, SAUSA300_1753 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2FFT4, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

-
Non-polymers , 5 types, 469 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32.5 % PEG 400, 0.3 M Ammonium Sulphate pH = 3.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 77687 / % possible obs: 92.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 6.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 13.9 / Num. unique obs: 10882 / % possible all: 88.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4VID

4vid


Resolution: 1.7→29.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.79 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.11
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 3888 5 %RANDOM
Rwork0.1674 ---
obs0.1694 73794 92.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.7 Å2 / Biso mean: 27.698 Å2 / Biso min: 13.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0.68 Å2-0.34 Å2
2---0.28 Å2-0.14 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.7→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5897 0 115 451 6463
Biso mean--52.97 35.51 -
Num. residues----789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0136237
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175570
X-RAY DIFFRACTIONr_angle_refined_deg2.051.6428483
X-RAY DIFFRACTIONr_angle_other_deg1.5831.57313017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.185809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62825.56259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16315973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.379156
X-RAY DIFFRACTIONr_chiral_restr0.1120.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.026983
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021163
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 251 -
Rwork0.181 5239 -
all-5490 -
obs--88.15 %
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)
10.53870.0094-0.30931.444-0.07910.80880.0465-0.0152-0.07940.0665-0.0196-0.042-0.1630.0497-0.02690.0357-0.01050.00510.070.00590.029721.12233.71266.712
20.54870.20770.45511.31810.4511.97810.1035-0.03950.09440.0795-0.06120.04290.3655-0.173-0.04230.0703-0.0345-0.00920.05450.01350.0429-5.7175-24.12475.5848
31.28560.22220.53370.74810.1040.8342-0.0540.03990.037-0.04470.04810.053-0.06440.07880.0060.0405-0.0196-0.00870.0140.00460.00539.5504-6.6827-23.1922
41.82360.50440.22550.76440.0320.60580.02640.0775-0.02280.0916-0.0037-0.08870.021-0.0589-0.02270.0553-0.0241-0.0060.0260.00030.0139-15.0361-35.786-23.708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 203
2X-RAY DIFFRACTION2B1 - 203
3X-RAY DIFFRACTION3C2 - 203
4X-RAY DIFFRACTION4D2 - 203

+
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