[English] 日本語
Yorodumi
- PDB-6ifq: Crystal structure of a standalone versatile EAL protein from Vibr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ifq
TitleCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - Apo form
Componentscyclic di nucleotide phoshodiesterase
KeywordsHYDROLASE / cyclic dinucleotide phosphodiesterase / nucleotide binding
Function / homologyPutative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / nucleotide binding / metal ion binding / EAL domain-containing protein
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsYadav, M. / Pal, K. / Sen, U.
CitationJournal: Biochem.J. / Year: 2019
Title: Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication.
Authors: Yadav, M. / Pal, K. / Sen, U.
History
DepositionSep 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: cyclic di nucleotide phoshodiesterase
A: cyclic di nucleotide phoshodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1304
Polymers58,0502
Non-polymers802
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-34 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.701, 42.812, 73.573
Angle α, β, γ (deg.)90.000, 94.610, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein cyclic di nucleotide phoshodiesterase


Mass: 29025.090 Da / Num. of mol.: 2 / Mutation: C15S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_A1247 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H3AJ04, cyclic-guanylate-specific phosphodiesterase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, sodium citrate, ammonium acetate / PH range: 7.4-8.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.95→78.59 Å / Num. obs: 35579 / % possible obs: 98.7 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.026 / Rrim(I) all: 0.048 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-23.60.614889324850.920.3830.7261.999.4
8.94-78.592.70.03110133800.9960.0250.0436.992

-
Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementResolution: 1.95→51.588 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.47
RfactorNum. reflection% reflection
Rfree0.2575 1818 5.14 %
Rwork0.2069 --
obs0.2094 35358 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 198.15 Å2 / Biso mean: 83.4184 Å2 / Biso min: 34.97 Å2
Refinement stepCycle: final / Resolution: 1.95→51.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 2 52 3844
Biso mean--61.97 57.03 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083876
X-RAY DIFFRACTIONf_angle_d0.955226
X-RAY DIFFRACTIONf_chiral_restr0.044574
X-RAY DIFFRACTIONf_plane_restr0.004682
X-RAY DIFFRACTIONf_dihedral_angle_d14.9771428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.00270.3921300.32352546267698
2.0027-2.06170.34431320.30162568270098
2.0617-2.12820.32461520.28362584273699
2.1282-2.20430.27891420.26082554269698
2.2043-2.29250.26221520.24022577272998
2.2925-2.39690.32751500.23742557270798
2.3969-2.52320.27971330.23862592272598
2.5232-2.68130.29171410.23342569271098
2.6813-2.88830.27341230.22992610273398
2.8883-3.1790.24481440.23022579272398
3.179-3.63890.25061470.20132465261294
3.6389-4.58420.2211560.17552640279699
4.5842-51.60620.25281160.17862699281597
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)
17.09990.02581.87572.8718-0.31363.2141-0.01020.2390.0846-0.34630.0582-0.7787-0.5311.5709-0.08220.6331-0.3640.06781.1491-0.09110.555430.153-2.288810.4113
25.52921.8062.55412.961-2.41515.6265-0.16230.4172-0.4305-0.36910.2979-0.71050.49411.8415-0.21710.4252-0.0477-0.03431.2017-0.11930.597329.9955-11.345213.7851
36.10611.87261.72548.38990.24033.69070.1211-0.1707-0.5968-0.3487-0.1831-0.8610.96351.2601-0.01670.59250.2376-0.00040.83360.09780.587125.5104-17.312310.6831
42.4874-2.05720.74324.10561.40838.08060.15680.00790.0254-0.4176-0.1952-0.0365-0.58020.26050.03960.4703-0.1091-0.00810.32380.00350.321412.0873-5.02860.1896
58.84532.34283.84596.1952-0.20984.2933-0.6715-0.30681.37750.34790.1350.7046-1.49160.47040.861.1176-0.4317-0.00410.6566-0.46020.72417.09168.195814.6548
68.20392.14450.1684.2677-1.74456.46140.1150.1578-0.33760.0895-0.3512-0.96630.97211.50970.07490.63920.2307-0.07440.98730.00210.548426.2871-18.4227-32.2607
72.05860.6035-1.01731.47370.36478.54410.07510.1808-0.03350.0510.0295-0.15770.3330.5692-0.12340.50990.0366-0.07130.3773-0.00870.360715.1923-14.3313-23.8052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 21 through 70 )B21 - 70
2X-RAY DIFFRACTION2chain 'B' and (resid 71 through 108 )B71 - 108
3X-RAY DIFFRACTION3chain 'B' and (resid 109 through 151 )B109 - 151
4X-RAY DIFFRACTION4chain 'B' and (resid 152 through 239 )B152 - 239
5X-RAY DIFFRACTION5chain 'B' and (resid 240 through 257 )B240 - 257
6X-RAY DIFFRACTION6chain 'A' and (resid 21 through 85 )A21 - 85
7X-RAY DIFFRACTION7chain 'A' and (resid 86 through 257 )A86 - 257

+
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