7VLM | pdb_00007vlm

crystal structure of anti-CRISPR protein AcrIIA18

PDB DOI: https://doi.org/10.2210/pdb7VLM/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Streptococcus macedonicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-10-04 Released: 2021-12-01
Deposition Author(s): Zhang, H., Wang, X.S., Li, X.Z.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free:
0.202 (Depositor), 0.204 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7VLM

This is version 1.3 of the entry. See complete history.

Literature

Inhibition mechanisms of CRISPR-Cas9 by AcrIIA17 and AcrIIA18

Wang, X., Li, X., Ma, Y., He, J., Liu, X., Yu, G., Yin, H., Zhang, H.

(2022) Nucleic Acids Res 50: 512-521

DOI: https://doi.org/10.1093/nar/gkab1197

Macromolecule Content

Total Structure Weight: 21.61 kDa
Atom Count: 1,692
Modeled Residue Count: 177
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H2C7	A	182	Streptococcus macedonicus	Mutation(s): 0 Gene Names: CS010_10295
UniProt
Find proteins for A0A2G3NPZ8 (Streptococcus macedonicus) Explore A0A2G3NPZ8 Go to UniProtKB: A0A2G3NPZ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2G3NPZ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain B [auth A]	B [auth A], E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free: 0.202 (Depositor), 0.204 (DCC)
R-Value Work: 0.182 (Depositor), 0.182 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.371	α = 90
b = 32.405	β = 120.366
c = 62.594	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
PHENIX	model building
Coot	model building
HKL-3000	data scaling
HKL-3000	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2021-12-01
Type: Initial release
Version 1.1: 2021-12-15
Changes: Database references, Structure summary
Version 1.2: 2023-07-05
Changes: Database references
Version 1.3: 2024-10-30
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.