[English] 日本語
Yorodumi
- PDB-7yib: Crystal structure of wild-type Cap4 SAVED domain-containing recep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yib
TitleCrystal structure of wild-type Cap4 SAVED domain-containing receptor from Enterobacter cloacae
ComponentsCD-NTase-associated protein 4
KeywordsHYDROLASE / SAVED domain-containing protein
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / nucleotide binding / DNA binding / metal ion binding / CD-NTase-associated protein 4
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.18 Å
AuthorsKo, T.-P. / Yang, C.-S. / Hou, M.-H. / Wang, Y.-C. / Chen, Y.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2311-B241-001 Taiwan
Ministry of Science and Technology (MoST, Taiwan)111-2311-B-039-001-MY3 Taiwan
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Specific recognition of cyclic oligonucleotides by Cap4 for phage infection.
Authors: Chang, J.J. / You, B.J. / Tien, N. / Wang, Y.C. / Yang, C.S. / Hou, M.H. / Chen, Y.
History
DepositionJul 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CD-NTase-associated protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6392
Polymers56,6031
Non-polymers351
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area22330 Å2
Unit cell
Length a, b, c (Å)150.958, 70.947, 56.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-501-

CL

21A-932-

HOH

-
Components

#1: Protein CD-NTase-associated protein 4 / Cap4 / Endodeoxyribonuclease Cap4


Mass: 56603.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: cap4, P853_02261 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DUD5, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 0.2 M sodium chloride, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.979, 0.979, 0.954
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9541
ReflectionResolution: 2.18→30 Å / Num. obs: 60956 / % possible obs: 99.6 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 43.13
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 5.95 / Num. unique obs: 3126 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1_3660phasing
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.18→26.44 Å / SU ML: 0.1796 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1998 3064 5.03 %
Rwork0.1656 57892 -
obs0.1673 60956 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.57 Å2
Refinement stepCycle: LAST / Resolution: 2.18→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 0 373 4314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00234027
X-RAY DIFFRACTIONf_angle_d0.56565458
X-RAY DIFFRACTIONf_chiral_restr0.0439595
X-RAY DIFFRACTIONf_plane_restr0.0034725
X-RAY DIFFRACTIONf_dihedral_angle_d17.87991489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.210.2421240.21552394X-RAY DIFFRACTION89.48
2.21-2.250.28371350.21232527X-RAY DIFFRACTION96.24
2.25-2.280.22241410.20282628X-RAY DIFFRACTION99.25
2.29-2.330.23011340.2012657X-RAY DIFFRACTION99.86
2.33-2.370.25931380.18652625X-RAY DIFFRACTION100
2.37-2.420.21031400.18142666X-RAY DIFFRACTION100
2.42-2.470.23881430.18612664X-RAY DIFFRACTION100
2.47-2.530.21221390.1812641X-RAY DIFFRACTION100
2.53-2.590.22461460.18832671X-RAY DIFFRACTION99.93
2.59-2.660.20651410.19362624X-RAY DIFFRACTION100
2.66-2.740.24941450.19362650X-RAY DIFFRACTION100
2.74-2.830.23151380.19822698X-RAY DIFFRACTION99.96
2.83-2.930.25511410.18862619X-RAY DIFFRACTION100
2.93-3.050.2141380.18512639X-RAY DIFFRACTION100
3.05-3.190.2391370.18632660X-RAY DIFFRACTION100
3.19-3.350.19091430.17042660X-RAY DIFFRACTION100
3.35-3.560.1971410.162645X-RAY DIFFRACTION99.86
3.56-3.840.17391380.15252643X-RAY DIFFRACTION99.93
3.84-4.220.22331400.13722635X-RAY DIFFRACTION100
4.22-4.830.13841390.12062654X-RAY DIFFRACTION99.79
4.83-6.070.17381420.15872675X-RAY DIFFRACTION99.86
6.08-26.440.17761410.16452617X-RAY DIFFRACTION99.07
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)
11.96798731511-1.163662660050.9151704660931.77694568636-0.9151160115210.9493073453420.08663943616580.04615610648150.00973928139995-0.110814677391-0.0486900198885-0.06605051319650.07207322776950.0310978116730.0002244774307170.255754656410.01750501526250.06238732134350.2695495853890.03538070085990.2884367139561.060156477516.096190539215.1277972329
21.09301225969-0.114564525467-0.3492493935520.375475340409-0.478236317420.3819809672390.005266831885840.09064881540340.372947479334-0.0670179764233-0.122114427421-0.01690758821840.02448346242620.00739945658775-0.05625713809780.3692263182710.02851393656160.01824493527890.3653459440050.08610471567010.34815627046649.520895911132.08886819097.07579731986
33.178625991360.55673366669-0.5841590476621.114063958730.3761501552431.1281715683-0.0783001974468-0.01130099086580.0872343822545-0.0574751055339-0.06168210936960.1924181137980.164761657234-0.0235469647107-3.36823039496E-50.3354766510860.02660334443950.00161454644080.284858538389-0.0483830911540.27989984998624.553625522921.764530090418.4950868801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 192 )
2X-RAY DIFFRACTION2chain 'A' and (resid 193 through 287 )
3X-RAY DIFFRACTION3chain 'A' and (resid 288 through 499 )

+
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