[English] 日本語
Yorodumi
- PDB-7ci1: Crystal structure of AcrVA2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ci1
TitleCrystal structure of AcrVA2
ComponentsAcrVA2
KeywordsHYDROLASE INHIBITOR / CRISPR-Cas / AcrVA2 / Cpf1 / Cas12a / MbCpf1 / MbCas12a / MbCprf1 / anti-CRISPR / Acr
Function / homologySPERMIDINE
Function and homology information
Biological speciesMoraxella bovoculi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsChen, P. / Cheng, Z. / Wang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91440201 China
National Natural Science Foundation of China (NSFC)31700662 China
CitationJournal: Prog.Biochem.Biophys. / Year: 2021
Title: Structural Study on Anti-CRISPR Protein AcrVA2
Authors: Chen, P. / Sun, W. / Cheng, Z. / Yang, J. / Wang, M. / Wang, J. / Chen, H. / Liu, L. / Wang, Y.
History
DepositionJul 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Dec 30, 2020Group: Structure summary / Category: struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.3Jan 13, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value
Revision 1.4Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.5Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AcrVA2
B: AcrVA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,75414
Polymers73,7602
Non-polymers99412
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint28 kcal/mol
Surface area29420 Å2
Unit cell
Length a, b, c (Å)84.287, 84.287, 264.171
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 2 or resid 4...
d_2ens_1(chain "B" and (resid 0 through 2 or resid 4...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERHISA1 - 3
d_12ens_1THRASPA5 - 188
d_13ens_1GLYLYSA190 - 234
d_14ens_1THRVALA236 - 258
d_15ens_1ARGILEA262 - 266
d_16ens_1HISALAA270 - 298
d_21ens_1SERHISD1 - 3
d_22ens_1THRASPD7 - 190
d_23ens_1GLYLYSD192 - 236
d_24ens_1THRVALD238 - 260
d_25ens_1ARGILED264 - 268
d_26ens_1HISALAD271 - 299

-
Components

#1: Protein AcrVA2


Mass: 36879.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella bovoculi (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.085 M Hepes pH7.5, 1.7% PEG400, 1.7 M (NH4)2SO4, 15% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 46743 / % possible obs: 99.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 26.65 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.022 / Rrim(I) all: 0.072 / Χ2: 0.94 / Net I/σ(I): 31.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 2 / Num. unique obs: 2349 / CC1/2: 0.649 / Rpim(I) all: 0.342 / Rrim(I) all: 0.93 / Χ2: 0.843 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→48.97 Å / SU ML: 0.2908 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 27.7577
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 2002 4.97 %
Rwork0.2292 38303 -
obs0.2303 40305 86.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4655 0 66 135 4856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184862
X-RAY DIFFRACTIONf_angle_d1.69046590
X-RAY DIFFRACTIONf_chiral_restr0.2403714
X-RAY DIFFRACTIONf_plane_restr0.0079838
X-RAY DIFFRACTIONf_dihedral_angle_d21.24161725
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.546282394432 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3093610.25741080X-RAY DIFFRACTION34.52
2.36-2.430.2886670.2611465X-RAY DIFFRACTION45.87
2.43-2.50.3106940.28231837X-RAY DIFFRACTION57.83
2.5-2.580.26791130.28132399X-RAY DIFFRACTION76.05
2.58-2.670.2681780.2782976X-RAY DIFFRACTION95.06
2.67-2.780.30761600.27463179X-RAY DIFFRACTION99.61
2.78-2.90.28011920.2553166X-RAY DIFFRACTION100
2.9-3.060.27531400.26063165X-RAY DIFFRACTION100
3.06-3.250.3051840.24223169X-RAY DIFFRACTION99.97
3.25-3.50.24981380.22993197X-RAY DIFFRACTION99.97
3.5-3.850.22311560.21273192X-RAY DIFFRACTION100
3.85-4.410.18561710.19473143X-RAY DIFFRACTION99.94
4.41-5.550.22241760.19293161X-RAY DIFFRACTION99.88
5.55-48.970.26251720.2123174X-RAY DIFFRACTION99.35

+
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