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1rvy

E75Q MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE

Method: X-RAY DIFFRACTION Dmax: 93.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine hydroxymethyltransferase, cytosolic

Oryctolagus cuniculus

UniProt P07511

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：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

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 1RVY 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
1RV3 E75L MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE Deposited 2003-12-12 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：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 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：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 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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1rvy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1rvy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1rvy
Deposition date deposition_date2003-12-15
Structure title titleE75Q MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE
Keywords keywordsONE CARBON METABOLISM, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.27 Å
Radius of gyration Rg (electron density) rg_electron28.32 Å
Forward intensity I(0) i0172549000.00
Molecular weight molecular_weight102800.0 kDa
Excluded volume excluded_volume128020 ų
Envelope volume envelope_volume151200 ų
Hydration-shell volume shell_volume42846 ų
Envelope diameter envelope_diameter99.5 Å
Shell Rg shell_rg37.17 Å
Envelope Rg envelope_rg28.60 Å
Shape Rg shape_rg28.31 Å
Total Rg total_rg29.10 Å
Total atoms total_atoms7226
Residues n_residues929
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax93.6 Å
Rg (real space) rg_real29.18 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real1.7250e+08
I(0) uncertainty (real space) i0_real_error2.6080e+06
Rg (reciprocal space) rg_reciprocal29.22 Å
I(0) (reciprocal space) i0_reciprocal172600000.0000
Solution quality estimate total_estimate0.8925
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.7 Å
Skewness Skewness skewness0.289
Kurtosis Kurtosis kurtosis-0.316
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha61600000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.943
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1rvya_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.4 — GABA-aminotransferase-like
Domain ID domain_idd1rvyb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamilyc.67.1 — PLP-dependent transferases
Family Family familyc.67.1.4 — GABA-aminotransferase-like

CATH v4.4 (4 domains)

Domain ID domain_id1rvyA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily10 — Aspartate Aminotransferase, domain 1
Domain ID domain_id1rvyA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)
Domain ID domain_id1rvyB01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily10 — Aspartate Aminotransferase, domain 1
Domain ID domain_id1rvyB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)
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8. Citations (1)

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9. Files and Curves (10)