[English] 日本語
Yorodumi
- PDB-8iy2: Structure of Acb2 complexed with 3',3'-cGAMP and cAAA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8iy2
TitleStructure of Acb2 complexed with 3',3'-cGAMP and cAAA
Componentsp26
KeywordsVIRAL PROTEIN / anti-CBASS protein
Function / homologyChem-3AM / GUANOSINE-3'-MONOPHOSPHATE / p26
Function and homology information
Biological speciesPseudomonas phage PaP2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsCao, X.L. / Xiao, Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol.Cell / Year: 2024
Title: Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides.
Authors: Cao, X. / Xiao, Y. / Huiting, E. / Cao, X. / Li, D. / Ren, J. / Fedorova, I. / Wang, H. / Guan, L. / Wang, Y. / Li, L. / Bondy-Denomy, J. / Feng, Y.
History
DepositionApr 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: p26
B: p26
C: p26
D: p26
E: p26
F: p26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,40245
Polymers63,5046
Non-polymers9,89939
Water45025
1
A: p26
hetero molecules

A: p26
hetero molecules

A: p26
hetero molecules

A: p26
hetero molecules

A: p26
hetero molecules

A: p26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,13454
Polymers63,5046
Non-polymers11,63048
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
2
B: p26
hetero molecules

B: p26
hetero molecules

B: p26
hetero molecules

B: p26
hetero molecules

B: p26
hetero molecules

B: p26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,76148
Polymers63,5046
Non-polymers11,25742
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
3
C: p26
D: p26
hetero molecules

C: p26
D: p26
hetero molecules

C: p26
D: p26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,63042
Polymers63,5046
Non-polymers9,12636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
4
E: p26
F: p26
hetero molecules

E: p26
F: p26
hetero molecules

E: p26
F: p26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,63042
Polymers63,5046
Non-polymers9,12636
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Unit cell
Length a, b, c (Å)103.427, 103.427, 101.487
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21D-304-

HOH

31D-306-

HOH

-
Components

#1: Protein
p26 / Acb2


Mass: 10583.947 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage PaP2 (virus) / Gene: orf26 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PVL0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical...
ChemComp-3AM / [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate / 3'-AMP


Mass: 347.221 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-3GP / GUANOSINE-3'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium bromide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 16565 / % possible obs: 99.7 % / Redundancy: 9.8 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.042 / Rrim(I) all: 0.133 / Χ2: 1.223 / Net I/σ(I): 7.7 / Num. measured all: 162997
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.76-2.818.90.9548240.8860.9690.3341.0121.068100
2.81-2.869.30.9028050.8720.9650.3080.9541.07999.6
2.86-2.919.10.7238250.910.9760.250.7661.09199.6
2.91-2.9710.10.6718080.9370.9840.2190.7071.098100
2.97-3.0410.60.5268220.9570.9890.1670.5531.11499.6
3.04-3.1110.10.4768050.9740.9930.1540.51.05699.8
3.11-3.1910.10.3768140.9840.9960.1230.3961.04599.6
3.19-3.279.40.3218250.9620.990.1090.3391.199.9
3.27-3.3710.40.2818200.9820.9950.090.2951.07599.8
3.37-3.4810.10.248220.9880.9970.0780.2531.14399.9
3.48-3.69.60.1938260.9920.9980.0650.2041.16299.8
3.6-3.7510.40.1388220.9950.9990.0440.1451.18799.9
3.75-3.9210.20.18300.99810.0330.1051.17799.8
3.92-4.129.40.0848320.9980.9990.0280.0881.25699.8
4.12-4.3810.40.0728190.99910.0230.0761.34798.8
4.38-4.729.90.0648310.99910.0210.0681.36499.6
4.72-5.1910.50.0688350.99910.0220.0721.36599.6
5.19-5.949.60.0668370.99810.0220.071.44699.9
5.94-7.489.80.058610.99910.0160.0521.58199.9
7.48-508.80.032902110.0110.0341.68898.4

-
Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→40.97 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2928 819 4.97 %
Rwork0.2438 --
obs0.2462 16472 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.76→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 52 25 5049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135149
X-RAY DIFFRACTIONf_angle_d2.0277018
X-RAY DIFFRACTIONf_dihedral_angle_d15.9361154
X-RAY DIFFRACTIONf_chiral_restr0.08767
X-RAY DIFFRACTIONf_plane_restr0.032819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.930.43371310.35282548X-RAY DIFFRACTION99
2.93-3.160.30971270.28722587X-RAY DIFFRACTION99
3.16-3.470.34151350.28412581X-RAY DIFFRACTION99
3.47-3.970.31981390.23462610X-RAY DIFFRACTION100
3.98-5.010.26161400.22072623X-RAY DIFFRACTION99
5.01-40.970.23671470.212704X-RAY DIFFRACTION99

+
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