SAXSdb — 1nbi

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

Glycine N-methyltransferase

Rattus norvegicus

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–292 Chain B； UniProt 1–292 Chain C； UniProt 1–292 Chain D； UniProt 1–292	Mutation：R175K	SAM S-ADENOSYLMETHIONINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；296 K；PEG 3400, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 3.00 Å R-free 0.295

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 1NBI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BHJ CRYSTAL STRUCTURE OF APO-GLYCINE N-METHYLTRANSFERASE (GNMT) Deposited 1998-06-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–292（292 aa） Chain B 1–292（292 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；pH 6.8	Resolution 2.50 Å R-free 0.318
1D2C METHYLTRANSFERASE Deposited 1999-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–293（292 aa） Chain B 2–293（292 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；277 K；PEG 3400, pH 5.6, VAPOR DIFFUSION, temperature 4.0K	Resolution 2.50 Å R-free 0.233
1D2C METHYLTRANSFERASE Deposited 1999-09-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–293（292 aa） Chain B 2–293（292 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；277 K；PEG 3400, pH 5.6, VAPOR DIFFUSION, temperature 4.0K	Resolution 2.50 Å R-free 0.233
1D2G CRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE FROM RAT LIVER Deposited 1999-10-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–293（292 aa） Fragment：WHOLE ENZYME Chain B 2–293（292 aa） Fragment：WHOLE ENZYME	Mutation：R175K Mutation：R175K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG-4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.266
1D2G CRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE FROM RAT LIVER Deposited 1999-10-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–293（292 aa） Fragment：WHOLE ENZYME Chain B 2–293（292 aa） Fragment：WHOLE ENZYME	Mutation：R175K Mutation：R175K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG-4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.266
1D2H CRYSTAL STRUCTURE OF R175K MUTANT GLYCINE N-METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLHOMOCYSTEINE Deposited 1999-10-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–293（292 aa） Fragment：WHOLE ENZYME Chain B 2–293（292 aa） Fragment：WHOLE ENZYME Chain C 2–293（292 aa） Fragment：WHOLE ENZYME Chain D 2–293（292 aa） Fragment：WHOLE ENZYME	Mutation：R175K Mutation：R175K Mutation：R175K Mutation：R175K	SAH S-ADENOSYL-L-HOMOCYSTEINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG-4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.247
1KIA Crystal structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate Deposited 2001-12-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–292（292 aa） Chain B 1–292（292 aa） Chain C 1–292（292 aa） Chain D 1–292（292 aa）	Not recorded	ACT ACETATE ION × 4 SAM S-ADENOSYLMETHIONINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.80 Å R-free 0.286
1NBH Structure of glycine N-methyltransferase complexed with S-adenosylmethionine and acetate, GNMT:SAM:Ace Deposited 2002-12-02	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–292（292 aa） Chain B 1–292（292 aa） Chain C 1–292（292 aa） Chain D 1–292（292 aa）	Not recorded	ACT ACETATE ION × 4 SAM S-ADENOSYLMETHIONINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；296 K；PEG 3400, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.80 Å R-free 0.278
1XVA METHYLTRANSFERASE Deposited 1996-07-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–292（292 aa） Chain B 1–292（292 aa）	Not recorded	ACT ACETATE ION × 4 SAM S-ADENOSYLMETHIONINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.20 Å R-free 0.262
2IDJ Crystal Structure of Rat Glycine N-Methyltransferase Apoprotein, Monoclinic Form Deposited 2006-09-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–292（292 aa） Chain B 1–292（292 aa） Chain C 1–292（292 aa） Chain D 1–292（292 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；20% PEG 3350, 0.1 M Ca acetate, 0.025 M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.35 Å R-free 0.272
2IDK Crystal Structure of Rat Glycine N-Methyltransferase Complexed With Folate Deposited 2006-09-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–292（292 aa） Chain B 1–292（292 aa） Chain C 1–292（292 aa） Chain D 1–292（292 aa）	Not recorded	C2F 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；20% PEG 3350, 0.1 M Ca acetate, 0.025 M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.55 Å R-free 0.298
3THR Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate monoglutamate Deposited 2011-08-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–293（292 aa） Chain B 2–293（292 aa） Chain C 2–293（292 aa） Chain D 2–293（292 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	C2F 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 4 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；20% PEG 3350, 0.2 M Na-fluoride or Ca-acetate, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.00 Å R-free 0.241
3THS Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate pentaglutamate Deposited 2011-08-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–293（292 aa） Chain B 2–293（292 aa） Chain C 2–293（292 aa） Chain D 2–293（292 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	BME BETA-MERCAPTOETHANOL × 1 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；20% PEG 3350, 0.2 M Na-fluoride or Ca-acetate, 100 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.50 Å R-free 0.280

11 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GNMT_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–292； UniProt 1–292 Author chain B； PDBConstruct 1–292； UniProt 1–292 Author chain C； PDBConstruct 1–292； UniProt 1–292 Author chain D； PDBConstruct 1–292； UniProt 1–292

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	1nbi
Deposition date deposition_date	2002-12-02
Structure title title	Structure of R175K mutated glycine N-methyltransferase complexed with S-adenosylmethionine, R175K:SAM.
Keywords keywords	Methyltransferase, Glycine N-methyltransferase, Catalytic mechanism, Dynamical catalysis, 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	36.58 Å
Radius of gyration Rg (electron density) rg_electron	35.89 Å
Forward intensity I(0) i0	236945000.00
Molecular weight molecular_weight	124050.0 kDa
Excluded volume excluded_volume	154960 Å³
Envelope volume envelope_volume	203560 Å³
Hydration-shell volume shell_volume	46615 Å³
Envelope diameter envelope_diameter	108.8 Å
Shell Rg shell_rg	43.58 Å
Envelope Rg envelope_rg	34.36 Å
Shape Rg shape_rg	35.89 Å
Total Rg total_rg	36.42 Å
Total atoms total_atoms	8740
Residues n_residues	1100
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	111.7 Å
Rg (real space) rg_real	36.39 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	2.3690e+08
I(0) uncertainty (real space) i0_real_error	3.4560e+06
Rg (reciprocal space) rg_reciprocal	36.51 Å
I(0) (reciprocal space) i0_reciprocal	237000000.0000
Solution quality estimate total_estimate	0.9094
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	54.5 Å
Skewness Skewness skewness	0.031
Kurtosis Kurtosis kurtosis	-0.725
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	82130000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.969

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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	Glycine N-methyltransferase
Molecular weight formula_weight	32432.8 kDa
EC 编号 ec_number	2.1.1.20
Mutation mutation	R175K
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8984

VDSVYRTRSLGVAAEGIPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRKEPAFDKWVIEEANWLTLDKDVPAGDGFDAVICLGNSFAHLPDSKGDQSEHRLALKNIASMVRPGGLLVIDHKNYDYILSTGCAPPGKNIYYKSDLTKDITTSVLTVNNKAHMVTLDYTVQVPGAGRDGAPGFSKFRLSYYPHCLASFTELVQEAFGGRCQHSVLGDFKPYRPGQAYVPCYFIHVLKKTG

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1nbia_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

Domain ID domain_id	d1nbib_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

Domain ID domain_id	d1nbic_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

Domain ID domain_id	d1nbid_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.5 — Glycine N-methyltransferase

CATH v4.4 (8 domains)

Domain ID domain_id	1nbiA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1nbiA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1nbiB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1nbiB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1nbiC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1nbiC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1nbiD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	46 — Glycine N-methyltransferase; chain A, domain 1
Homologous superfamily homologous superfamily	10 — Glycine N-methyltransferase, chain A, domain 1

Domain ID domain_id	1nbiD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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8. Citations (1)

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Unit-cell length a length_a	77.870 Å
Unit-cell length b length_b	77.870 Å
Unit-cell length c length_c	227.130 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
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1660
R_work r_work	0.1650
R_free r_free	0.2950

fit	/app/data/saxs_computation/nb/1nbi/1nbi.fit
pddf	/app/data/pr_computation/nb/1nbi/1nbi.pr.out
profile	/app/data/saxs_computation/nb/1nbi/1nbi.dat

Structure of R175K mutated glycine N-methyltransferase complexed with S-adenosylmethionine, R175K:SAM.

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

Glycine N-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