SAXSdb — 1cj0

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

PROTEIN (SERINE HYDROXYMETHYLTRANSFERASE)

Oryctolagus cuniculus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 14–485 Chain B； UniProt 14–485	Mutation：N5Q	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；20MM K2HPO4, KH2PO4, 25MM POTASIUM MES OR SODIUM HEPES, PH 7.0 0.2 MM 2-MERCAPTOETHANOL, 3% PEG 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.80 Å R-free 0.280

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 1CJ0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RV3 E75L MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE Deposited 2003-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–483（483 aa） Chain B 1–483（483 aa）	Mutation：E75L Mutation：E75L	PO4 PHOSPHATE ION × 4 PLP PYRIDOXAL-5'-PHOSPHATE × 4 GLY GLYCINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；PEG 8000, KCl, potassium phosphate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.40 Å R-free 0.255
1RV4 E75L MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE Deposited 2003-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–483（483 aa） Chain B 1–483（483 aa）	Mutation：E75L Mutation：E75L	PO4 PHOSPHATE ION × 4 PLP PYRIDOXAL-5'-PHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；298 K；PEG 8000, KCl, potassium phosphate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.95 Å R-free 0.241
1RVU E75Q MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE Deposited 2003-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–483（483 aa） Chain B 1–483（483 aa）	Mutation：E75Q Mutation：E75Q	PLP PYRIDOXAL-5'-PHOSPHATE × 4 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；PEG 4000, KCl, KMES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.50 Å R-free 0.250
1RVY E75Q MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE Deposited 2003-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–483（483 aa） Chain B 1–483（483 aa）	Mutation：E75Q Mutation：E75Q	PLG N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] × 2 PO4 PHOSPHATE ION × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；PEG 4000, KCl, KMES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.K	Resolution 2.90 Å R-free 0.283

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

View Construct and Data Evidence

UniProt name	GLYC_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–470； UniProt 14–485 Author chain B； PDBConstruct 1–470； UniProt 14–485

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	1cj0
Deposition date deposition_date	1999-04-20
Structure title title	CRYSTAL STRUCTURE OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE AT 2.8 ANGSTROM RESOLUTION
Keywords keywords	HYDROXYMETHYL TRANSFERASE, 1 CARBON METABOLISM, 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	29.25 Å
Radius of gyration Rg (electron density) rg_electron	28.18 Å
Forward intensity I(0) i0	165948000.00
Molecular weight molecular_weight	99654.0 kDa
Excluded volume excluded_volume	123490 Å³
Envelope volume envelope_volume	148190 Å³
Hydration-shell volume shell_volume	42266 Å³
Envelope diameter envelope_diameter	96.7 Å
Shell Rg shell_rg	36.96 Å
Envelope Rg envelope_rg	28.46 Å
Shape Rg shape_rg	28.20 Å
Total Rg total_rg	28.89 Å
Total atoms total_atoms	7012
Residues n_residues	930
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	92.1 Å
Rg (real space) rg_real	29.16 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.6590e+08
I(0) uncertainty (real space) i0_real_error	2.3970e+06
Rg (reciprocal space) rg_reciprocal	29.20 Å
I(0) (reciprocal space) i0_reciprocal	166000000.0000
Solution quality estimate total_estimate	0.8960
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.1 Å
Skewness Skewness skewness	0.285
Kurtosis Kurtosis kurtosis	-0.331
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	58280000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.929

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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	PROTEIN (SERINE HYDROXYMETHYLTRANSFERASE)
Molecular weight formula_weight	51706.8 kDa
Mutation mutation	N5Q
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	7024

WSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF

来源 Source

来源生物 organism	Oryctolagus cuniculus
通用名 common_name	rabbit
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 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	12

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cj0a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.4 — GABA-aminotransferase-like

Domain ID domain_id	d1cj0b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.4 — GABA-aminotransferase-like

CATH v4.4 (4 domains)

Domain ID domain_id	1cj0A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1cj0A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	1cj0B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	1cj0B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

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8. Citations (1)

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Unit-cell length a length_a	116.380 Å
Unit-cell length b length_b	116.380 Å
Unit-cell length c length_c	165.380 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2140
R_free r_free	0.2800

fit	/app/data/saxs_computation/cj/1cj0/1cj0.fit
pddf	/app/data/pr_computation/cj/1cj0/1cj0.pr.out
profile	/app/data/saxs_computation/cj/1cj0/1cj0.dat

CRYSTAL STRUCTURE OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE AT 2.8 ANGSTROM RESOLUTION

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

PROTEIN (SERINE HYDROXYMETHYLTRANSFERASE)

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