[English] 日本語
Yorodumi
- PDB-6jl0: Crystal structure of VvPlpA from Vibrio vulnificus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jl0
TitleCrystal structure of VvPlpA from Vibrio vulnificus
ComponentsThermolabile hemolysin
KeywordsHYDROLASE / Vibrio / phospholipase / SGNH hydrolase
Function / homologyLipase, GDSL, active site / Lipolytic enzymes "G-D-S-L" family, serine active site. / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / lipase activity / SGNH hydrolase superfamily / lipid metabolic process / BROMIDE ION / Thermolabile hemolysin
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.073 Å
AuthorsMa, Q. / Wan, Y. / Liu, C.
Funding support China, 2items
OrganizationGrant numberCountry
Other government1000 talent program China
Chinese Academy of Sciences100 talent program China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural analysis of aVibriophospholipase reveals an unusual Ser-His-chloride catalytic triad.
Authors: Wan, Y. / Liu, C. / Ma, Q.
History
DepositionMar 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Aug 14, 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.title / _citation_author.identifier_ORCID
Revision 1.3Apr 3, 2024Group: 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: Thermolabile hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2092
Polymers48,1301
Non-polymers801
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.865, 53.865, 232.287
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Thermolabile hemolysin


Mass: 48129.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: CRN61_10355 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S3SYP4
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5 mg/ml protein in 10 mM HEPES, 150 mM NaBr, pH 7.5, was mixed with equal volume reservoir solution (200 mM potassium sodium tartrate tetrahydrate, 180 mM NDSB-201, 12% polyethylene glycol ...Details: 5 mg/ml protein in 10 mM HEPES, 150 mM NaBr, pH 7.5, was mixed with equal volume reservoir solution (200 mM potassium sodium tartrate tetrahydrate, 180 mM NDSB-201, 12% polyethylene glycol 1500, and 10% glycerine)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9163 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 2.073→45.736 Å / Num. obs: 24564 / % possible obs: 99.1 % / Redundancy: 18.2 % / CC1/2: 0.998 / Rpim(I) all: 0.019 / Rrim(I) all: 0.082 / Rsym value: 0.079 / Net I/σ(I): 20.9
Reflection shellResolution: 2.073→2.109 Å / Redundancy: 12 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 998 / CC1/2: 0.896 / Rpim(I) all: 0.185 / Rrim(I) all: 0.684 / Rsym value: 0.656 / % possible all: 86.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: our own model

Resolution: 2.073→45.735 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.98
RfactorNum. reflection% reflection
Rfree0.2268 2284 5.06 %
Rwork0.1907 --
obs0.1926 24562 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.073→45.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 1 117 3309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143291
X-RAY DIFFRACTIONf_angle_d1.3014486
X-RAY DIFFRACTIONf_dihedral_angle_d12.4651895
X-RAY DIFFRACTIONf_chiral_restr0.084475
X-RAY DIFFRACTIONf_plane_restr0.011576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.073-2.1180.32091230.28322222X-RAY DIFFRACTION84
2.118-2.16730.29681390.24982714X-RAY DIFFRACTION98
2.1673-2.22150.26071240.22062685X-RAY DIFFRACTION100
2.2215-2.28160.25191400.23392691X-RAY DIFFRACTION100
2.2816-2.34870.31081900.22952718X-RAY DIFFRACTION100
2.3487-2.42450.32961220.22042681X-RAY DIFFRACTION100
2.4245-2.51120.29911180.21742708X-RAY DIFFRACTION100
2.5112-2.61170.23511480.2062726X-RAY DIFFRACTION100
2.6117-2.73050.23091240.21112773X-RAY DIFFRACTION100
2.7305-2.87450.26151340.21522706X-RAY DIFFRACTION100
2.8745-3.05450.23561360.2122706X-RAY DIFFRACTION100
3.0545-3.29030.22541680.1982682X-RAY DIFFRACTION100
3.2903-3.62130.21451630.18752717X-RAY DIFFRACTION100
3.6213-4.1450.20171600.16362709X-RAY DIFFRACTION100
4.145-5.22110.1821480.15332699X-RAY DIFFRACTION100
5.2211-45.74640.21481470.18172709X-RAY DIFFRACTION100
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)
13.0648-0.4535-0.7842.2901-0.26526.1271-0.221-0.033-0.2591-0.07670.07820.53730.0823-0.27390.34340.4619-0.1198-0.04550.58350.00720.5245-4.5612-8.560613.2862
22.42861.09910.01051.00810.02531.6046-0.06260.10240.1167-0.19330.05870.00740.0436-0.0751-0.00240.4763-0.1379-0.04270.43070.02710.371116.6119-0.88924.5703
31.28971.0545-0.27491.2828-0.75550.7182-0-0.16340.0877-0.0059-0.02960.0251-0.00660.01260.02580.428-0.1471-0.0090.466-0.02550.395220.5002-3.590118.0923
40.8961-0.0392-0.68370.066-0.24251.67670.4604-0.25280.40710.597-0.15290.32010.098-0.2998-0.15170.6352-0.08030.02240.8110.00730.785613.04927.087929.2077
52.0902-0.11290.77531.9011-0.73142.1508-0.0335-0.39360.11150.0542-0.01190.2378-0.0964-0.11440.07620.3489-0.19720.02030.5403-0.02450.320512.1808-11.132127.7793
60.5980.56080.26362.21250.18561.26730.2307-0.47990.02480.0311-0.3569-0.0987-0.09310.01090.11370.4662-0.3036-0.0370.78280.07430.409927.0377-10.266736.3741
71.2910.91360.10931.49770.25691.12630.1197-0.18830.0977-0.0014-0.0964-0.2151-0.15850.2723-0.0120.3706-0.1552-0.00380.5120.02370.360834.154-3.618322.6598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 24:41)
2X-RAY DIFFRACTION2(chain A and resid 42:138)
3X-RAY DIFFRACTION3(chain A and resid 139:206)
4X-RAY DIFFRACTION4(chain A and resid 207:214)
5X-RAY DIFFRACTION5(chain A and resid 215:281)
6X-RAY DIFFRACTION6(chain A and resid 282:342)
7X-RAY DIFFRACTION7(chain A and resid 343:421)

+
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