SAXSdb — 3kzy

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

Methylated-DNA--protein-cysteine methyltransferase

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–182	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；34% PEG 3350, 100mM BisTris pH 5.5, 500mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.261
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–182	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；34% PEG 3350, 100mM BisTris pH 5.5, 500mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.261

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 3KZY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6RLA Structure of the dynein-2 complex; motor domains Deposited 2019-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 5–181（177 aa） Chain B 5–181（177 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6RLB Structure of the dynein-2 complex; tail domain Deposited 2019-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 5–181（177 aa） Chain B 5–181（177 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
6SC2 Structure of the dynein-2 complex; IFT-train bound model Deposited 2019-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 5–181（177 aa） Chain B 5–181（177 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6Y8P Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore Deposited 2020-03-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–182（176 aa）	Not recorded	ZN ZINC ION × 1 OGQ [9-[2-carboxy-5-[(4-methylphenyl)methylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；100 mM Na HEPES pH 7.5 25% PEG 8000 10 mg/mL protein 100 nl:100 nL	Resolution 2.30 Å R-free 0.277
8DD7 The Cryo-EM structure of Drosophila Cryptochrome in complex with Timeless Deposited 2022-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–181（181 aa） Chain B 5–181（177 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å
8TK7 Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 360 PDB declaration: 360-meric	Chain D 1–182（182 aa） Chain E 1–182（182 aa） Chain F 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；150 mM NaCl, 20 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
8TK7 Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–182（182 aa） Chain E 1–182（182 aa） Chain F 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；150 mM NaCl, 20 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
8TK7 Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain D 1–182（182 aa） Chain E 1–182（182 aa） Chain F 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；150 mM NaCl, 20 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
8TK7 Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain D 1–182（182 aa） Chain E 1–182（182 aa） Chain F 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；150 mM NaCl, 20 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
8TK7 Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–182（182 aa） Chain E 1–182（182 aa） Chain F 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；150 mM NaCl, 20 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
9DI0 Cryo-EM structure of Kif18A bound to a microtubule Deposited 2024-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 5–181（177 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 TA1 TAXOL × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	E5BBQ0_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–182； UniProt 1–182 Author chain B； PDBConstruct 1–182； UniProt 1–182

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	3kzy
Deposition date deposition_date	2009-12-09
Structure title title	Crystal structure of SNAP-tag
Keywords keywords	protein tag, protein engineering, benzylguanine, TRANSFERASE; TRANSFERASE
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	22.34 Å
Radius of gyration Rg (electron density) rg_electron	21.30 Å
Forward intensity I(0) i0	20456500.00
Molecular weight molecular_weight	35279.0 kDa
Excluded volume excluded_volume	44563 Å³
Envelope volume envelope_volume	53641 Å³
Hydration-shell volume shell_volume	21161 Å³
Envelope diameter envelope_diameter	74.6 Å
Shell Rg shell_rg	27.88 Å
Envelope Rg envelope_rg	21.33 Å
Shape Rg shape_rg	21.31 Å
Total Rg total_rg	22.20 Å
Total atoms total_atoms	2484
Residues n_residues	324
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	72.1 Å
Rg (real space) rg_real	22.29 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	2.0460e+07
I(0) uncertainty (real space) i0_real_error	2.6400e+05
Rg (reciprocal space) rg_reciprocal	22.31 Å
I(0) (reciprocal space) i0_reciprocal	20460000.0000
Solution quality estimate total_estimate	0.7153
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.414
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3453000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 0.189; Positv: 1.000; Valcen: 1.000; Smooth: 0.989

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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	Methylated-DNA--protein-cysteine methyltransferase
Molecular weight formula_weight	19437.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2759

GPGSDKDCEMKRTTLDSPLGKLELSGCEQGLHEIIFLGKGTSAADAVEVPAPAAVLGGPEPLMQATAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYSHLAALAGNPAATAAVKTALSGNPVPILIPCHRVVQGDLDVGGYEGGLAVKEWLLAHEGHRLGKR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	251

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3kzya1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.7 — Methylated DNA-protein cysteine methyltransferase domain
Family Family family	c.55.7.0 — automated matches

Domain ID domain_id	d3kzya2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.2 — Methylated DNA-protein cysteine methyltransferase, C-terminal domain
Family Family family	a.4.2.0 — automated matches

Domain ID domain_id	d3kzyb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.7 — Methylated DNA-protein cysteine methyltransferase domain
Family Family family	c.55.7.0 — automated matches

Domain ID domain_id	d3kzyb2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.2 — Methylated DNA-protein cysteine methyltransferase, C-terminal domain
Family Family family	a.4.2.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3kzyA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	70 — Methylated DNA-protein cysteine methyltransferase domain

Domain ID domain_id	3kzyA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	3kzyB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	70 — Methylated DNA-protein cysteine methyltransferase domain

Domain ID domain_id	3kzyB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	112.535 Å
Unit-cell length b length_b	112.535 Å
Unit-cell length c length_c	64.823 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	31.200 Å
R factor r_factor	0.2071
R_work r_work	0.2042
R_free r_free	0.2614

fit	/app/data/saxs_computation/kz/3kzy/3kzy.fit
pddf	/app/data/pr_computation/kz/3kzy/3kzy.pr.out
profile	/app/data/saxs_computation/kz/3kzy/3kzy.dat

Crystal structure of SNAP-tag

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

Methylated-DNA--protein-cysteine methyltransferase

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