SAXSdb — 1rv3

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

Serine hydroxymethyltransferase, cytosolic

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–483 Chain B； UniProt 1–483	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

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 1RV3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CJ0 CRYSTAL STRUCTURE OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE AT 2.8 ANGSTROM RESOLUTION Deposited 1999-04-20	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 14–485（472 aa） Chain B 14–485（472 aa）	Mutation：N5Q 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
1RV4 E75L MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE Deposited 2003-12-12	Different ligand/ion 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–483（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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–483（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 1–483； UniProt 1–483 Author chain B； PDBConstruct 1–483； UniProt 1–483

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	1rv3
Deposition date deposition_date	2003-12-12
Structure title title	E75L MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE
Keywords keywords	ONE-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	29.42 Å
Radius of gyration Rg (electron density) rg_electron	28.45 Å
Forward intensity I(0) i0	172855000.00
Molecular weight molecular_weight	102790.0 kDa
Excluded volume excluded_volume	128020 Å³
Envelope volume envelope_volume	153350 Å³
Hydration-shell volume shell_volume	43256 Å³
Envelope diameter envelope_diameter	100.7 Å
Shell Rg shell_rg	37.19 Å
Envelope Rg envelope_rg	28.71 Å
Shape Rg shape_rg	28.45 Å
Total Rg total_rg	29.22 Å
Total atoms total_atoms	7224
Residues n_residues	929
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	95.6 Å
Rg (real space) rg_real	29.33 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	1.7290e+08
I(0) uncertainty (real space) i0_real_error	2.4760e+06
Rg (reciprocal space) rg_reciprocal	29.37 Å
I(0) (reciprocal space) i0_reciprocal	172900000.0000
Solution quality estimate total_estimate	0.6786
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.4 Å
Skewness Skewness skewness	0.285
Kurtosis Kurtosis kurtosis	-0.317
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	63520000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 0.092; Positv: 1.000; Valcen: 0.995; Smooth: 0.956

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Serine hydroxymethyltransferase, cytosolic
Molecular weight formula_weight	52900.2 kDa
EC 编号 ec_number	2.1.2.1
Mutation mutation	E75L
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	7327

ATAVNGAPRDAALWSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSLGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF

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	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	GLYCINE
Molecular weight formula_weight	75.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	86

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1rv3a_
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	d1rv3b_
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	1rv3A01
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	1rv3A02
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	1rv3B01
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	1rv3B02
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	114.920 Å
Unit-cell length b length_b	114.920 Å
Unit-cell length c length_c	158.290 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	2.400 Å
Low-resolution limit resolution_low	48.880 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2550

fit	/app/data/saxs_computation/rv/1rv3/1rv3.fit
pddf	/app/data/pr_computation/rv/1rv3/1rv3.pr.out
profile	/app/data/saxs_computation/rv/1rv3/1rv3.dat

E75L MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE

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

Serine hydroxymethyltransferase, cytosolic

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