[English] 日本語
Yorodumi
- PDB-6oft: The crystal structure of the first half of the periplasmic protea... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oft
TitleThe crystal structure of the first half of the periplasmic protease PqqL from Escherichia coli
ComponentsProbable zinc protease PqqL
KeywordsHYDROLASE / Protease / M16 Family / Processing Protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / metallopeptidase activity / peptidase activity / outer membrane-bounded periplasmic space / proteolysis / zinc ion binding / cytosol
Similarity search - Function
: / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like
Similarity search - Domain/homology
PHOSPHATE ION / Probable zinc protease PqqL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGrinter, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust106077/Z/14/Z United Kingdom
CitationJournal: PLoS Genet / Year: 2019
Title: Protease-associated import systems are widespread in Gram-negative bacteria.
Authors: Rhys Grinter / Pok Man Leung / Lakshmi C Wijeyewickrema / Dene Littler / Simone Beckham / Robert N Pike / Daniel Walker / Chris Greening / Trevor Lithgow /
Abstract: Bacteria have evolved sophisticated uptake machineries in order to obtain the nutrients required for growth. Gram-negative plant pathogens of the genus Pectobacterium obtain iron from the protein ...Bacteria have evolved sophisticated uptake machineries in order to obtain the nutrients required for growth. Gram-negative plant pathogens of the genus Pectobacterium obtain iron from the protein ferredoxin, which is produced by their plant hosts. This iron-piracy is mediated by the ferredoxin uptake system (Fus), a gene cluster encoding proteins that transport ferredoxin into the bacterial cell and process it proteolytically. In this work we show that gene clusters related to the Fus are widespread in bacterial species. Through structural and biochemical characterisation of the distantly related Fus homologues YddB and PqqL from Escherichia coli, we show that these proteins are analogous to components of the Fus from Pectobacterium. The membrane protein YddB shares common structural features with the outer membrane ferredoxin transporter FusA, including a large extracellular substrate binding site. PqqL is an active protease with an analogous periplasmic localisation and iron-dependent expression to the ferredoxin processing protease FusC. Structural analysis demonstrates that PqqL and FusC share specific features that distinguish them from other members of the M16 protease family. Taken together, these data provide evidence that protease associated import systems analogous to the Fus are widespread in Gram-negative bacteria.
History
DepositionApr 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable zinc protease PqqL
B: Probable zinc protease PqqL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8058
Polymers108,3602
Non-polymers4456
Water7,116395
1
A: Probable zinc protease PqqL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4385
Polymers54,1801
Non-polymers2584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable zinc protease PqqL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3673
Polymers54,1801
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.070, 84.440, 92.070
Angle α, β, γ (deg.)90.00, 102.24, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Probable zinc protease PqqL


Mass: 54179.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pqqL, yddC, b1494, JW1489 / Production host: Escherichia coli (E. coli) / Strain (production host): C41
References: UniProt: P31828, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThis domain of PqqL was crystallised by in situ Trypsination of the full-length protein. This was ...This domain of PqqL was crystallised by in situ Trypsination of the full-length protein. This was the sequence of the purified protein that was added to the drop (With a small quantity of Trypsin): AALPQDEKLITGQLDNGLRYMIYPHAHPKDQVNLWLQIHTGSLQEEDNELGVAHFVEHMMFNGTKTWPGNKVIETFESMGLRFGRDVNAYTSYDETVYQVSLPTTQKQNLQQVMAIFSEWSNAATFEKLEVDAERGVITEEWRAHQDAKWRTSQARRPFLLANTRNLDREPIGLMDTVATVTPAQLRQFYQRWYQPNNMTFIVVGDIDSKEALALIKDNLSKLPANKAAENRVWPTKAENHLRFNIINDKENRVNGIALYYRLPMVQVNDEQSFIEQAEWSMLVQLFNQRLQERIQSGELKTISGGTARSVKIAPDYQSLFFRVNARDDNMQDAANALMAELATIDQHGFSAEELDDVKSTRLTWLKNAVDQQAERDLRMLTSRLASSSLNNTPFLSPEETYQLSKRLWQQITVQSLAEKWQQLRKNQDAFWEQMVNNEVAAKKALSPAAILALEKEYANKKLAAYVFPGRNLSLTVDADPQAEISSKETLAENLTSLTLSNGARVILAKSAGEEQKLQIIAVSNKGDLSFPAQQKSLIALANKAVSGSGVGELSSSSLKRWSAENSVTMSSKVSGMNTLLSVSARTNNPEPGFQLINQRITHSTINDNIWASLQNAQIQALKTLDQRPAEKFAQQMYETRYADDRTKLLQENQIAQFTAADALAADRQLFSSPADITFVIVGNVAEDKLVALITRYLGSIKHSDSPLAAGKPLTRATDNASVTVKEQNEPVAQVSQWKRYDSRTPVNLPTRMALDAFNVALAKDLRVNIREQASGAYSVSSRLSVDPQAKDISHLLAFTCQPERHDELLTLANEVMVKRLAKGISEQELNEYQQNVQRSLDIQQRSVQQLANTIVNSLIQYDDPAAWTEQEQLLKQMTVENVNTAVKQYLSHPVNTYTGVLLPKLEHHHHHH The most likely cleavage point for Trypsin is ARG497, meaning the protein in the crystal consists of the first 497 amino acids, minus the first 26 amino acids as reported.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.6 % / Description: Diamond Shaped Plates
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.2
Details: 0.1 M phosphate-citrate buffer, 0.2 M NaCl, 20% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Mar 8, 2016 / Details: Yes
RadiationMonochromator: Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→21.36 Å / Num. obs: 71853 / % possible obs: 99.8 % / Observed criterion σ(I): 1.7 / Redundancy: 22.3 % / Biso Wilson estimate: 32.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.348 / Rpim(I) all: 0.07 / Net I/σ(I): 14.4
Reflection shellResolution: 2→2.04 Å / Redundancy: 15.1 % / Rmerge(I) obs: 2.009 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4575 / CC1/2: 0.61 / Rpim(I) all: 0.531 / % possible all: 99

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AMJ

3amj


Resolution: 2→21.36 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.171 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3563 4.96 %RANDOM
Rwork0.193 ---
obs0.194 71806 99.9 %-
Displacement parametersBiso mean: 37.35 Å2
Baniso -1Baniso -2Baniso -3
1-5.4602 Å20 Å2-1.2585 Å2
2---8.124 Å20 Å2
3---2.6637 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2→21.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7593 0 17 398 8008
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097762HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0210526HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2767SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1347HARMONIC5
X-RAY DIFFRACTIONt_it7762HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion18.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion999SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9045SEMIHARMONIC4
LS refinement shellResolution: 2→2.01 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.219 -5.5 %
Rwork0.2353 1358 -
all0.2344 1437 -
obs--99.59 %
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)
10.5428-0.40320.21880.441-0.10070.6060.01530.0441-0.0561-0.02630.00660.0444-0.0150.0131-0.0219-0.0152-0.02110.0167-0.0556-0.0054-0.072267.069619.402934.9638
21.93640.467-0.99890.3151-0.03020.69080.08430.15260.0262-0.0166-0.00110.0604-0.1623-0.088-0.0832-0.0290.0024-0.0107-0.04470.0401-0.168667.9852-11.081810.7341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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