PDB-9j1z: Crystal structure of Nme1Cas9 HNH domain bound to anti-CRISPR Acr...

ID or keywords:

Entry

Database: PDB / ID: 9j1z

Title

Crystal structure of Nme1Cas9 HNH domain bound to anti-CRISPR AcrIIC1Nme1ST

Components

AcrIIC1Nme1ST
CRISPR-associated endonuclease Cas9

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 / AB INITIO PHASING / Resolution: 1.91 Å

Authors

Xiao, Y. / Wang, Z.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of NmeCas9 HNH domain bound to anti-CRISPR AcrIIC1Nme1ST
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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Download

PDBx/mmCIF format	9j1z.cif.gz	189.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9j1z.ent.gz	148.6 KB	Display	PDB format
PDBx/mmJSON format	9j1z.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/j1/9j1z ftp://data.pdbj.org/pub/pdb/validation_reports/j1/9j1z	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

B: CRISPR-associated endonuclease Cas9

C: AcrIIC1Nme1ST

A: CRISPR-associated endonuclease Cas9

D: AcrIIC1Nme1ST

58.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: CRISPR-associated endonuclease Cas9

C: AcrIIC1Nme1ST

defined by author&software
Evidence: gel filtration
29 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: CRISPR-associated endonuclease Cas9

D: AcrIIC1Nme1ST

defined by author&software
29 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	45.961, 47.633, 61.716
Angle α, β, γ (deg.)	107.44, 97.49, 115.25
Int Tables number	1
Space group name H-M	P1

#1: Protein	CRISPR-associated endonuclease Cas9 Mass: 17837.979 Da / Num. of mol.: 2 / 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	AcrIIC1Nme1ST Mass: 11210.491 Da / Num. of mol.: 2 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.: 271 / 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: 1.91 Å³/Da / Density % sol: 35.76 %
Crystal grow	Temperature: 289.15 K / Method: batch mode Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 10% w/v Polyethylene glycol 6,000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL02U1 / Wavelength: 0.97918 Å

Detector

Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 15, 2023

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 32382 / % possible obs: 97.8 % / Redundancy: 3.4 % / CC_1/2: 0.963 / CC star: 0.99 / R_merge(I) obs: 0.079 / R_pim(I) all: 0.049 / R_rim(I) all: 0.093 / Χ²: 0.817 / Net I/σ(I): 30.3 / Num. measured all: 111483

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
1.9-1.93	2.7	0.277	1553	0.89	0.97	0.197	0.342	1.223	95.8
1.93-1.97	3	0.258	1636	0.894	0.972	0.177	0.315	1.112	96.5
1.97-2.01	3.3	0.225	1567	0.945	0.986	0.142	0.267	0.999	96.5
2.01-2.05	3.5	0.188	1627	0.967	0.991	0.116	0.221	1.034	96.8
2.05-2.09	3.6	0.162	1590	0.969	0.992	0.099	0.191	0.956	97
2.09-2.14	3.6	0.139	1606	0.978	0.994	0.085	0.164	0.924	97.2
2.14-2.19	3.6	0.133	1627	0.975	0.994	0.082	0.156	0.887	97.5
2.19-2.25	3.5	0.115	1617	0.978	0.994	0.072	0.137	0.916	97.4
2.25-2.32	3.5	0.096	1600	0.983	0.996	0.06	0.113	0.785	97.8
2.32-2.39	3.3	0.085	1621	0.978	0.994	0.056	0.103	0.789	97.4
2.39-2.48	3.4	0.078	1607	0.986	0.996	0.049	0.092	0.716	98.1
2.48-2.58	3.6	0.073	1624	0.987	0.997	0.044	0.086	0.737	98.1
2.58-2.7	3.6	0.067	1631	0.987	0.997	0.041	0.079	0.664	98.1
2.7-2.84	3.4	0.062	1647	0.986	0.997	0.039	0.073	0.69	98.6
2.84-3.02	3.5	0.056	1621	0.985	0.996	0.035	0.066	0.612	98.7
3.02-3.25	3.7	0.056	1655	0.989	0.997	0.034	0.065	0.622	98.7
3.25-3.58	3.6	0.055	1638	0.986	0.996	0.034	0.065	0.617	99
3.58-4.09	3.4	0.048	1639	0.989	0.997	0.03	0.057	0.561	99.3
4.09-5.16	3.5	0.049	1639	0.987	0.997	0.031	0.058	0.555	99.5
5.16-50	3.5	0.109	1637	0.929	0.981	0.068	0.129	1.154	99

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Processing

Software

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

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.91→28.95 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 2 / Phase error: 21.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2168	1625	5.06 %
R_work	0.1819	-	-
obs	0.1837	32129	96.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.91→28.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3439	0	0	271	3710

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3481
X-RAY DIFFRACTION	f_angle_d	0.631	4694
X-RAY DIFFRACTION	f_dihedral_angle_d	4.586	479
X-RAY DIFFRACTION	f_chiral_restr	0.044	495
X-RAY DIFFRACTION	f_plane_restr	0.01	608

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 (%)
1.91-1.97	0.2696	97	0.2005	2122	X-RAY DIFFRACTION	80
1.97-2.03	0.2537	137	0.1928	2477	X-RAY DIFFRACTION	96
2.03-2.1	0.2161	132	0.1812	2585	X-RAY DIFFRACTION	96
2.1-2.19	0.2147	117	0.1839	2611	X-RAY DIFFRACTION	97
2.19-2.29	0.2269	135	0.1814	2565	X-RAY DIFFRACTION	97
2.29-2.41	0.2369	151	0.1749	2558	X-RAY DIFFRACTION	98
2.41-2.56	0.2194	140	0.191	2581	X-RAY DIFFRACTION	98
2.56-2.76	0.2251	120	0.1972	2592	X-RAY DIFFRACTION	98
2.76-3.03	0.2246	125	0.1966	2623	X-RAY DIFFRACTION	99
3.03-3.47	0.2129	151	0.1858	2592	X-RAY DIFFRACTION	99
3.47-4.37	0.2029	166	0.1601	2596	X-RAY DIFFRACTION	99
4.37-28.95	0.2011	154	0.1787	2602	X-RAY DIFFRACTION	99

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	0.0089	-0.0203	-0.0029	0.0304	0.0067	0.0011	0.0475	-0.0317	-0.0806	-0.1864	0.0223	-0.1433	-0.0018	-0.018	0.0002	0.2617	-0.0808	0.0042	0.2046	0.0302	0.2679	18.892	-26.3659	-24.4856
2	0.1591	0.0084	0.0708	0.2937	-0.1782	0.1455	0.0389	-0.0482	0.0215	-0.0339	0.1925	0.2812	-0.068	-0.1541	0.3007	-0.0882	-0.0615	-0.0361	0.0829	0.0155	0.1444	21.4652	-21.082	-12.3025
3	0.1201	-0.0857	-0.1037	0.0512	0.0099	0.5098	0.0493	-0.0656	0.0232	0.0316	-0.0164	-0.0087	-0.1324	-0.0137	0.009	0.0118	-0.0151	0.0023	0.0416	0.0086	0.0256	32.4582	-13.3136	-10.7299
4	0.343	0.0295	0.0925	0.2864	-0.2651	0.3548	-0.1525	-0	0.2271	-0.0614	-0.1024	-0.3078	-0.0039	0.2159	-0.3522	-0.0467	-0.0399	-0.0336	0.0904	-0.0027	0.1676	44.8858	-14.4724	-14.2132
5	0.0701	0.0062	-0.0213	0.0352	-0.0383	0.0629	0.0059	-0.0497	0.1013	0.0964	0.0999	0.1095	-0.1158	-0.0873	0.0054	0.1112	0.0151	-0.0007	0.0689	-0.0108	0.0739	23.8884	1.0559	-11.0632
6	0.0018	0.0029	0	-0.0002	0.0006	0.0033	0.0407	-0.0047	-0.0183	-0.0027	-0.0367	-0.0641	0.0819	-0	0	0.3938	0.1484	0.0017	0.4888	-0.0783	0.4046	23.5071	-7.0283	-28.0324
7	0.0424	-0.0068	-0.0047	0.1004	-0.0132	0.0516	0.0141	-0.0243	-0.0054	-0.0748	0.0395	0.098	0.0401	-0.0036	0.0675	0.0788	0.1024	-0.1197	0.4663	-0.1284	0.2006	13.9194	2.4824	-20.5845
8	0.022	0.0292	0.0275	0.0389	0.0293	0.0306	0.097	0.0068	0.0862	0.0224	0.0465	-0.0544	-0.1683	-0.0688	0.0579	0.0888	0.0236	0.0204	0.053	0.0102	0.0637	25.1161	3.8106	-15.3687
9	0.0316	0.0093	0.0162	0.0015	0.004	0.0129	-0.1549	0.0439	0.0237	0.0547	0.0183	0.0096	-0.0283	-0.0362	-0.0129	0.2957	-0.0276	-0.0747	0.2782	-0.0287	0.2313	18.6641	-11.6161	-43.1009
10	0.1165	-0.1169	-0.0759	0.2331	-0.0896	0.2857	0.0361	0.0233	-0.0216	-0.1407	-0.0025	0.025	0.2296	0.0598	0.0497	0.0836	0.0029	-0.0059	0.0349	0.0076	0.0314	38.1617	-9.4414	-45.9699
11	0.0433	-0.0149	0.0204	0.2277	-0.0282	0.0227	-0.0443	-0.1441	0.0739	0.2489	0.0097	-0.0461	-0.0925	0.0303	-0.0957	0.0642	-0.033	-0.0395	0.0695	-0.0092	0.0788	44.9864	-0.0954	-35.414
12	0.1447	-0.0092	0.0491	0.0231	-0.0406	0.1979	0.0435	-0.0385	-0.0687	-0.157	0.0564	-0.1679	0.0721	0.0211	0.0418	0.1214	0.0173	0.048	0.0446	0.0029	0.16	47.5696	-24.2189	-44.8476
13	0.0025	-0.0007	-0.0018	0.0049	-0.0077	0.0088	-0.0096	-0.0683	0.0777	0.0039	0.0511	0.0621	-0.0666	-0.0263	0	0.481	-0.1003	0.2251	0.5673	0.1327	0.5767	33.7908	-27.3814	-34.891
14	0.014	0.0067	0	0.1496	-0.0549	0.0432	-0.1174	0.0074	-0.1353	0.0599	-0.0019	0.0216	0.1921	0.0159	-0.0991	0.1636	0.066	0.0939	-0.1343	-0.0852	0.1238	45.0921	-30.4698	-42.3294

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 23 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 24 through 44 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 45 through 97 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 98 through 137 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 4 through 38 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 39 through 54 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 55 through 73 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 74 through 91 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1 through 23 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 24 through 97 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 98 through 137 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 4 through 37 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 38 through 61 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 62 through 91 )

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