PDB-9j1y: Crystal structure of Nme1Cas9 HNH domain bound to anti-CRISPR Acr...

ID or keywords:

Entry

Database: PDB / ID: 9j1y

Title

Crystal structure of Nme1Cas9 HNH domain bound to anti-CRISPR AcrIIC1Boe.

Components

CRISPR-associated endonuclease Cas9
anti-CRISPR AcrIIC1Boe

Keywords

HYDROLASE / Nme1Cas9 / Anti CRISPR

Function / homology

Function and homology information

maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function

Biological species

Neisseria meningitidis serogroup C (bacteria)

Bacteriophage sp. (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.79 Å

Authors

Xiao, Y. / Wang, Z.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Nme1Cas9 HNH domain bound to anti-CRISPR AcrIIC1Boe.
Authors: Xiao, Y. / Wang, Z.

History

Deposition	Aug 6, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Mar 4, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9j1y.cif.gz	114.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9j1y.ent.gz	86.7 KB	Display	PDB format
PDBx/mmJSON format	9j1y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j1/9j1y ftp://data.pdbj.org/pub/pdb/validation_reports/j1/9j1y	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#181 - Jan 2015 Cascade and CRISPR similarity (5)

Deposited unit

A: CRISPR-associated endonuclease Cas9

B: anti-CRISPR AcrIIC1Boe

29.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	61.753, 61.753, 50.032
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	CRISPR-associated endonuclease Cas9 Mass: 17426.523 Da / Num. of mol.: 1 / Fragment: HNH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup C (strain 8013) (bacteria) Gene: cas9, NMV_1993 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: C9X1G5, Hydrolases; Acting on ester bonds
#2: Protein	anti-CRISPR AcrIIC1Boe Mass: 11726.276 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteriophage sp. (virus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.89 Å³/Da / Density % sol: 34.9 %
Crystal grow	Temperature: 289.15 K / Method: batch mode Details: 200 nM ammonium sulfate, 100 mM sodium acetate (pH 4.5), 22% (w/v) PEG4000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.97776 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 3, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97776 Å / Relative weight: 1

Reflection

Resolution: 1.79→50 Å / Num. obs: 20145 / % possible obs: 100 % / Redundancy: 10.1 % / R_merge(I) obs: 0.146 / Net I/σ(I): 8.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.8-1.83	8.5	1.587	1021	0.731	0.919	0.57	1.689	0.71	100
1.83-1.86	10.1	1.354	1014	0.84	0.955	0.449	1.428	0.727	100
1.86-1.9	10.2	1.419	986	0.856	0.96	0.469	1.496	0.819	100
1.9-1.94	10.3	1.335	1038	0.854	0.96	0.441	1.407	1.336	100
1.94-1.98	10.4	0.713	977	0.935	0.983	0.233	0.75	0.839	100
1.98-2.03	10.3	0.604	1000	0.932	0.982	0.199	0.637	0.83	100
2.03-2.08	10.1	0.516	1013	0.952	0.987	0.17	0.544	1.071	99.9
2.08-2.13	9.9	0.374	999	0.97	0.992	0.125	0.394	0.944	100
2.13-2.2	9.3	0.321	1014	0.973	0.993	0.11	0.339	0.915	100
2.2-2.27	10	0.354	996	0.971	0.993	0.118	0.374	1.397	100
2.27-2.35	10.6	0.247	1028	0.984	0.996	0.08	0.26	0.928	100
2.35-2.44	10.6	0.199	986	0.986	0.997	0.064	0.209	0.927	100
2.44-2.55	10.5	0.182	998	0.988	0.997	0.059	0.191	0.928	100
2.55-2.69	10.3	0.159	1031	0.989	0.997	0.052	0.168	0.961	100
2.69-2.86	9.4	0.135	1011	0.987	0.997	0.046	0.143	0.95	99.9
2.86-3.08	10.9	0.122	1004	0.993	0.998	0.039	0.128	0.978	100
3.08-3.39	10.8	0.112	995	0.994	0.998	0.036	0.118	0.97	100
3.39-3.88	10.1	0.098	1020	0.992	0.998	0.033	0.103	0.966	99.9
3.88-4.88	9.9	0.088	1001	0.995	0.999	0.03	0.093	0.768	99.9
4.88-50	10.4	0.106	1013	0.992	0.998	0.034	0.111	0.856	100

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Processing

Software

Name	Version	Classification
PHENIX	(1.19_4092: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.79→36.54 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 20.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1906	1993	10 %
R_work	0.1575	-	-
obs	0.1608	19937	98.78 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.79→36.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1917	0	0	208	2125

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	1986
X-RAY DIFFRACTION	f_angle_d	0.687	2667
X-RAY DIFFRACTION	f_dihedral_angle_d	4.71	259
X-RAY DIFFRACTION	f_chiral_restr	0.045	266
X-RAY DIFFRACTION	f_plane_restr	0.005	351

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.79-1.83	0.3043	122	0.2126	1128	X-RAY DIFFRACTION	86
1.83-1.88	0.2397	150	0.2025	1261	X-RAY DIFFRACTION	99
1.88-1.94	0.2023	137	0.1786	1337	X-RAY DIFFRACTION	100
1.94-2	0.2018	135	0.1646	1288	X-RAY DIFFRACTION	100
2-2.07	0.2073	152	0.1693	1258	X-RAY DIFFRACTION	100
2.07-2.15	0.1846	154	0.1502	1311	X-RAY DIFFRACTION	100
2.16-2.25	0.1916	130	0.1515	1305	X-RAY DIFFRACTION	100
2.25-2.37	0.1938	156	0.1673	1299	X-RAY DIFFRACTION	100
2.37-2.52	0.1883	144	0.1671	1273	X-RAY DIFFRACTION	100
2.52-2.71	0.2025	148	0.1695	1294	X-RAY DIFFRACTION	100
2.72-2.99	0.2023	139	0.1706	1293	X-RAY DIFFRACTION	100
2.99-3.42	0.1974	143	0.1596	1315	X-RAY DIFFRACTION	100
3.42-4.31	0.1577	142	0.1314	1277	X-RAY DIFFRACTION	100
4.32-36.54	0.1711	141	0.1401	1305	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.0092	-0.0125	-0.0071	0.0128	-0.0023	0.0014	-0.0523	-0.0924	-0.061	0.1365	0.006	0.0028	0.1432	-0.0182	-0.0012	0.2844	0.0334	0.0112	0.3246	0.0685	0.1583	23.1259	-4.6176	51.948
2	0.0448	0.0165	0.0272	0.0072	0.0043	0.0306	-0.0148	-0.1922	0.0623	0.0686	0.005	-0.0155	0.0425	0.1959	-0.0064	0.0833	0.0157	-0.0016	0.2029	-0.0142	0.1336	23.4832	9.2525	45.8791
3	0.013	-0.0048	-0.0053	0.0081	-0.0059	0.0068	-0.014	0.0652	-0.0028	-0.0313	0.0313	-0.0153	-0.0301	0.0117	-0.0066	0.0651	-0.0098	0.0199	0.1146	0.0107	0.0862	18.4859	13.0961	35.642
4	0.0981	-0.0686	0.0362	0.1838	0.0674	0.374	-0.0036	0.055	0.0753	-0.0556	-0.0339	0.0588	-0.1782	-0.0563	-0.0658	0.1084	0.0014	-0.0128	0.083	-0.0063	0.0846	3.7457	14.2783	41.1838
5	0.0678	-0.0021	-0.0066	0.0358	0.0275	0.049	0.0164	0.1673	-0.0927	-0.0027	-0.1084	0.0796	-0.043	-0.1535	0.0079	0.0904	0.0169	-0.0021	0.111	-0.0337	0.0888	1.2789	6.1672	36.0795
6	0.007	0.0036	-0.0061	0.0109	0.0094	0.0147	0.0711	-0.0564	0.0986	-0.0768	0.005	-0.0041	-0.0591	0.0129	0.0089	0.1957	-0.04	0.0402	0.1133	-0.0308	0.2075	7.2286	26.2108	49.554
7	0.003	0.0071	-0.008	0.0265	-0.0336	0.0768	0.071	-0.1112	0.1871	-0.0121	-0.0358	-0.0519	-0.0934	0.0011	-0.0093	0.1649	-0.0469	0.0211	0.1665	-0.0885	0.208	11.726	26.0669	55.8647
8	0.0807	0.0545	-0.0585	0.0563	-0.03	0.048	-0.1157	-0.251	0.011	0.0754	0.0136	-0.1149	0.0002	0.0445	-0.0083	0.2123	-0.0093	-0.0259	0.2239	-0.006	0.0962	12.8795	10.5092	60.9641
9	0.1933	0.0705	0.2253	0.0288	0.0664	0.2521	0.0755	-0.1392	0.1608	0.0586	0.0661	-0.105	-0.0184	0.0738	0.2089	0.0917	-0.1567	-0.0154	0.1593	-0.2482	0.1578	13.1883	27.3022	62.7177
10	0.0277	-0.0255	0.0067	0.0242	-0.0064	0.0072	-0.0097	-0.039	0.0824	-0.0623	-0.0107	0.0578	0.0194	-0.0154	0.0012	0.1529	-0.0209	0.0005	0.0932	-0.0423	0.1342	4.4789	21.4161	51.7063

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 44 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 45 through 66 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 112 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 113 through 143 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 3 through 18 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 19 through 39 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 40 through 63 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 64 through 85 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 86 through 92 )

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