SAXSdb — 6kds

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

Alpha N-terminal protein methyltransferase 1B

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 61–283	Not recorded	CENP-A peptide × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8.1；291 K；0.1M Tris pH 8.1, 14% w/v Polyethylene glycol 8000	Resolution 1.84 Å R-free 0.205

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 6KDS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5UBB Crystal structure of human alpha N-terminal protein methyltransferase 1B Deposited 2016-12-20	Different construct 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 58–278（221 aa） Fragment：UNP residues 58-278	Not recorded	SAM S-ADENOSYLMETHIONINE × 2 UNX UNKNOWN LIGAND × 52	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M sodium acetate	Resolution 2.00 Å R-free 0.250
6DUB Crystal structure of a methyltransferase Deposited 2018-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 58–278（221 aa） Fragment：UNP residues 58-278	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 2 UNX UNKNOWN LIGAND × 37	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000, 0.1 M potassium thiocyanate	Resolution 1.20 Å R-free 0.178
6DUB Crystal structure of a methyltransferase Deposited 2018-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 58–278（221 aa） Fragment：UNP residues 58-278	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 23	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG2000, 0.1 M potassium thiocyanate	Resolution 1.20 Å R-free 0.178
6KDR Crystal structure of human NRMT2 in complex with human centromere protein B peptide Deposited 2019-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 61–283（223 aa） Fragment：Protein N-terminal methyltransferase Chain B 61–283（223 aa） Fragment：Protein N-terminal methyltransferase	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 GOL GLYCEROL × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；291 K；0.1M Tris pH 8.3, 6% w/v Polyethylene glycol 8000	Resolution 2.11 Å R-free 0.205

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NTM1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–244； UniProt 61–283

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	6kds
Deposition date deposition_date	2019-07-02
Structure title title	Crystal structure of human NRMT2 in complex with alpha-N-monomethylated human CENP-A peptide
Keywords keywords	core methyltransferase fold, 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	17.61 Å
Radius of gyration Rg (electron density) rg_electron	16.28 Å
Forward intensity I(0) i0	12327900.00
Molecular weight molecular_weight	26050.0 kDa
Excluded volume excluded_volume	32543 Å³
Envelope volume envelope_volume	36245 Å³
Hydration-shell volume shell_volume	17979 Å³
Envelope diameter envelope_diameter	54.1 Å
Shell Rg shell_rg	23.15 Å
Envelope Rg envelope_rg	16.66 Å
Shape Rg shape_rg	16.26 Å
Total Rg total_rg	17.39 Å
Total atoms total_atoms	1827
Residues n_residues	226
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	53.8 Å
Rg (real space) rg_real	17.45 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	1.2330e+07
I(0) uncertainty (real space) i0_real_error	1.3610e+05
Rg (reciprocal space) rg_reciprocal	17.47 Å
I(0) (reciprocal space) i0_reciprocal	12330000.0000
Solution quality estimate total_estimate	0.8961
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.7 Å
Skewness Skewness skewness	0.058
Kurtosis Kurtosis kurtosis	-0.467
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5723000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Alpha N-terminal protein methyltransferase 1B
Molecular weight formula_weight	27519.5 kDa
EC 编号 ec_number	2.1.1.299
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	2019

MGSSHHHHHHSSGLVPRGSHMVINGEMQFYARAKLFYQEVPATEEGMMGNFIELSSPDIQASQKFLRKFVGGPGRAGTDCALDCGSGIGRVSKHVLLPVFNSVELVDMMESFLLEAQNYLQVKGDKVESYHCYSLQEFTPPFRRYDVIWIQWVSGHLTDKDLLAFLSRCRDGLKENGIIILKDNVAREGCILDLSDSSVTRDMDILRSLIRKSGLVVLGQEKQDGFPEQCIPVWMFALHSDRHS

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 polymer

Description description	CENP-A peptide
Molecular weight formula_weight	744.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GPRRRS

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	167

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6kdsA00
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	62.603 Å
Unit-cell length b length_b	108.191 Å
Unit-cell length c length_c	38.799 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.844 Å
Low-resolution limit resolution_low	32.979 Å
R factor r_factor	0.1796
R_work r_work	0.1783
R_free r_free	0.2047

fit	/app/data/saxs_computation/kd/6kds/6kds.fit
pddf	/app/data/pr_computation/kd/6kds/6kds.pr.out
profile	/app/data/saxs_computation/kd/6kds/6kds.dat

Crystal structure of human NRMT2 in complex with alpha-N-monomethylated human CENP-A peptide

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

Alpha N-terminal protein methyltransferase 1B

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)