SAXSdb — 2nyu

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

Putative ribosomal RNA methyltransferase 2

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 51–246	Fragment：Residues 51-246 Mutation：C54S	SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；297 K；20% PEG 3350, 0.2M Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.76 Å R-free 0.281
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 51–246	Fragment：Residues 51-246 Mutation：C54S	SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；297 K；20% PEG 3350, 0.2M Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.76 Å R-free 0.281

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 2NYU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7O9K Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-Tu Deposited 2021-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 67 PDB declaration: 69-meric	Chain n 1–246（246 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 93 SAM S-ADENOSYLMETHIONINE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 PNS 4'-PHOSPHOPANTETHEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7O9M Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1 and the MALSU module Deposited 2021-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 66-meric	Chain n 1–246（246 aa）	Not recorded	MG MAGNESIUM ION × 104 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 1 PNS 4'-PHOSPHOPANTETHEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
7ODS State B of the human mitoribosomal large subunit assembly intermediate Deposited 2021-04-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 58-meric	Chain z 1–246（246 aa）	Not recorded	PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 88 K POTASSIUM ION × 8 N ANY 5'-MONOPHOSPHATE NUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；4 uL of the sample was blotted for 2-6 sec before plunging	Resolution 3.10 Å

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

View Construct and Data Evidence

UniProt name	RRMJ2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–196； UniProt 51–246 Author chain B； PDBConstruct 1–196； UniProt 51–246

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	2nyu
Deposition date deposition_date	2006-11-21
Structure title title	Crystal Structure of Human FtsJ homolog 2 (E.coli) protein in complex with S-adenosylmethionine
Keywords keywords	Transferase, SAM, ribosomal RNA, Structural Genomics, Structural Genomics Consortium, SGC; 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	23.50 Å
Radius of gyration Rg (electron density) rg_electron	22.73 Å
Forward intensity I(0) i0	26804100.00
Molecular weight molecular_weight	39785.0 kDa
Excluded volume excluded_volume	49933 Å³
Envelope volume envelope_volume	59174 Å³
Hydration-shell volume shell_volume	22397 Å³
Envelope diameter envelope_diameter	84.6 Å
Shell Rg shell_rg	28.73 Å
Envelope Rg envelope_rg	22.86 Å
Shape Rg shape_rg	22.75 Å
Total Rg total_rg	23.42 Å
Total atoms total_atoms	2803
Residues n_residues	362
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	81.7 Å
Rg (real space) rg_real	23.59 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	2.6800e+07
I(0) uncertainty (real space) i0_real_error	3.5690e+05
Rg (reciprocal space) rg_reciprocal	23.57 Å
I(0) (reciprocal space) i0_reciprocal	26800000.0000
Solution quality estimate total_estimate	0.8495
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.473
Kurtosis Kurtosis kurtosis	-0.232
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8406000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.710; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.985

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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	Putative ribosomal RNA methyltransferase 2
Molecular weight formula_weight	21710.8 kDa
EC 编号 ec_number	2.1.1.-
Mutation mutation	C54S
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	3042

SYRSRSAFKLLEVNERHQILRPGLRVLDCGAAPGAWSQVAVQKVNAAGTDPSSPVGFVLGVDLLHIFPLEGATFLCPADVTDPRTSQRILEVLPGRRADVILSDMAPNATGFRDLDHDRLISLCLTLLSVTPDILQPGGTFLCKTWAGSQSRRLQRRLTEEFQNVRIIKPEASRKESSEVYFLATQYHGRKGTVKQ

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

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	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	201

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2nyua_
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.66.1.0 — automated matches

Domain ID domain_id	d2nyub_
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.66.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2nyuA00
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	2nyuB00
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	102.022 Å
Unit-cell length b length_b	102.022 Å
Unit-cell length c length_c	37.068 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	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.760 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2275
R_work r_work	0.2264
R_free r_free	0.2811

fit	/app/data/saxs_computation/ny/2nyu/2nyu.fit
pddf	/app/data/pr_computation/ny/2nyu/2nyu.pr.out
profile	/app/data/saxs_computation/ny/2nyu/2nyu.dat

Crystal Structure of Human FtsJ homolog 2 (E.coli) protein in complex with S-adenosylmethionine

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

Putative ribosomal RNA methyltransferase 2

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