SAXSdb — 7enr

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1. Protein Identity and Related Structures Protein Identity & Related Structures

CRISPR-associated endonuclease Cas9

Staphylococcus aureus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–1053	Not recorded	sgRNA (98-MER) × 1 AcrIIA14 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289.15 K；PEG 3350, EG, Bicine	Resolution 4.21 Å R-free 0.307

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7ENR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5AXW Crystal structure of Staphylococcus aureus Cas9 in complex with sgRNA and target DNA (TTGGGT PAM) Deposited 2015-08-01	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–1053（1053 aa）	Mutation：N580A/C946A	NA SODIUM ION × 4 PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG4000, NaCl, Na2HPO4, NaN3	Resolution 2.70 Å R-free 0.230
5CZZ Crystal structure of Staphylococcus aureus Cas9 in complex with sgRNA and target DNA (TTGAAT PAM) Deposited 2015-08-01	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–1053（1053 aa）	Mutation：N580A/C946A	NA SODIUM ION × 5 PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG4000, NaCl, Na2HPO4, NaN3	Resolution 2.60 Å R-free 0.241
7EL1 Structure of a protein from bacteria Deposited 2021-04-07	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: pentameric	Chain A 1–1053（1053 aa）	Mutation：N580A, C946A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.0M sodium citrate dihydrate, 0.3M imidazol-Hcl (pH 10.0), 0.02M sodium malonate (pH 7.0)	Resolution 2.22 Å R-free 0.242
7ENH Crystal structure of cas and anti-cas protein complex Deposited 2021-04-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 481–646（166 aa） Fragment：HNH domain	Not recorded	NI NICKEL (II) ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；PEG 3350, sodium iodide	Resolution 2.10 Å R-free 0.208
7ENI Crystal structure of cas and anti-cas protein complex Deposited 2021-04-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain A 1–1053（1053 aa）	Not recorded	PO4 PHOSPHATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；Tris, Ammonium phosphate dibasic	Resolution 2.63 Å R-free 0.237
7VW3 Cryo-EM structure of SaCas9-sgRNA-DNA ternary complex Deposited 2021-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 2–1053（1052 aa）	Mutation：D10A N580A	MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20mM Tris-Cl (pH 7.5), 100mM KCl, 5mM MgCl2, 1mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8JFT Cryo-EM structure of SaCas9-AcrIIA15 CTD-sgRNA complex Deposited 2023-05-18	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain A 1–1053（1053 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.31 Å
8JG9 Cryo-EM structure of the SaCas9-sgRNA-AcrIIA15-promoter DNA dimer Deposited 2023-05-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: octameric	Chain A 1–1053（1053 aa） Chain D 1–1053（1053 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
8Y0D Crystal structure of SauCas9 in complex with sgRNA and 20nt ssDNA target Deposited 2024-01-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–1053（1053 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.2 M Sodium chloride, 0.1 M Sodium HEPES, pH 7.0, 11% PEG 8000	Resolution 3.92 Å R-free 0.318
8ZCY Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in an interrogation state Deposited 2024-04-30	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–1053（1053 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.17 Å
8ZCZ Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in an intermediate state Deposited 2024-04-30	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–1053（1053 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8ZD0 Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in a translocation state Deposited 2024-04-30	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–1053（1053 aa）	Not recorded	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å
8ZDA Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in a catalytically active state Deposited 2024-05-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric	Chain A 1–1053（1053 aa）	Not recorded	MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
9MB6 Cryo-EM structure of wild-type SaCas9-guide RNA-mismatched target DNA complex Deposited 2025-03-15	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–1053（1053 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9MB7 Cryo-EM structure of eSaCas9-NNG-guide RNA-mismatched target DNA complex Deposited 2025-03-15	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–1053（1053 aa）	Not recorded	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CAS9_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1053； UniProt 1–1053

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7enr
Deposition date deposition_date	2021-04-19
Structure title title	Crystal structure of cas and anti-cas protein complex
Keywords keywords	Inhibitor, Complex, VIRAL PROTEIN, VIRAL PROTEIN-RNA complex; VIRAL PROTEIN/RNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	39.56 Å
Radius of gyration Rg (electron density) rg_electron	39.08 Å
Forward intensity I(0) i0	455155000.00
Molecular weight molecular_weight	150170.0 kDa
Excluded volume excluded_volume	177790 Å³
Envelope volume envelope_volume	265950 Å³
Hydration-shell volume shell_volume	56800 Å³
Envelope diameter envelope_diameter	143.3 Å
Shell Rg shell_rg	44.95 Å
Envelope Rg envelope_rg	38.21 Å
Shape Rg shape_rg	39.12 Å
Total Rg total_rg	39.30 Å
Total atoms total_atoms	10487
Residues n_residues	1237
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	136.3 Å
Rg (real space) rg_real	39.60 Å
Rg uncertainty (real space) rg_real_error	1.17 Å
I(0) (real space) i0_real	4.5520e+08
I(0) uncertainty (real space) i0_real_error	8.1570e+06
Rg (reciprocal space) rg_reciprocal	39.58 Å
I(0) (reciprocal space) i0_reciprocal	455100000.0000
Solution quality estimate total_estimate	0.8816
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	44.3 Å
Skewness Skewness skewness	0.356
Kurtosis Kurtosis kurtosis	-0.294
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	61040000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.958

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CRISPR-associated endonuclease Cas9
Molecular weight formula_weight	124158.7 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10498

MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGARRLKRRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSAALLHLAKRRGVHNVNEVEEDTGNELSTKEQISRNSKALEEKYVAELQLERLKKDGEVRGSINRFKTSDYVKEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYEGPGEGSPFGWKDIKEWYEMLMGHCTYFPEELRSVKYAYNADLYNALNDLNNLVITRDENEKLEYYEKFQIIENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTSTGKPEFTNLKVYHDIKDITARKEIIENAELLDQIAKILTIYQSSEDIQEELTNLNSELTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNRLKLVPKKVDLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAREKNSKDAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYSLEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKGNRTPFQYLSSSDSKISYETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNLVDTRYATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKGYKHHAEDALIIANADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQEYKEIFITPHQIKHIKDFKDYKYSHRVDKKPNRELINDTLYSTRKDDKGNTLIVNNLNGLYDKDNDKLKKLINKSPEKLLMYHHDPQTYQKLKLIMEQYGDEKNPLYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSRNKVVKLSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQAEFIASFYNNDLIKINGELYRVIGVNNDLLNRIEVNMIDITYREYLENMNDKRPPRIIKTIASKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	sgRNA (98-MER)
Molecular weight formula_weight	31304.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

GGUCUGCUAUUUCUAUUUACGUUUUAGUACUCUGGAAACAGAAUCUACUAAAACAAGGCAAAAUGCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUC

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	AcrIIA14
Molecular weight formula_weight	11937.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MKSVKYISNMSKQEKGYRVYVNVVNEDTDKGFLFPSVPKEVIENDKIDELFNFEHHKPYVQKAKSRYDKNGIGYKIVQLDEGFQKFIELNKEKMKENLDY

来源 Source

来源生物 organism	Staphylococcus simulans
NCBI Class编号 ncbi_taxonomy_id	1286
宿主生物 host_organism	Escherichia coli BL21(DE3)

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8. Citations (1)

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Unit-cell length a length_a	173.800 Å
Unit-cell length b length_b	173.800 Å
Unit-cell length c length_c	185.894 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	4.205 Å
Low-resolution limit resolution_low	38.993 Å
R factor r_factor	0.2649
R_work r_work	0.2603
R_free r_free	0.3068

fit	/app/data/saxs_computation/en/7enr/7enr.fit
pddf	/app/data/pr_computation/en/7enr/7enr.pr.out
profile	/app/data/saxs_computation/en/7enr/7enr.dat

Crystal structure of cas and anti-cas protein complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

CRISPR-associated endonuclease Cas9

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)