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1d4f

CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE

Method: X-RAY DIFFRACTION Dmax: 112.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

S-ADENOSYLHOMOCYSTEINE HYDROLASE

Rattus norvegicus

UniProt P10760

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 1–431 Chain B； UniProt 1–431 Chain C； UniProt 1–431 Chain D； UniProt 1–431 Mutation：D244E NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADN ADENOSINE × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；22% PEG 4000, 50 mM Tris/HCl, 2% glycerol, 10% isopropanol, and 1 mM DTT. Protein concentration is 10 mg/mL., pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.80 Å R-free 0.248

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 1D4F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B3R RAT LIVER S-ADENOSYLHOMOCYSTEIN HYDROLASE Deposited 1998-12-14 Different construct 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 1–431（431 aa） Fragment：CATALYTIC DOMAIN (1 - 181 & 352 - 402)
Chain B 1–431（431 aa） Fragment：CATALYTIC DOMAIN (1 - 181 & 352 - 402)
Chain C 1–431（431 aa） Fragment：CATALYTIC DOMAIN (1 - 181 & 352 - 402)
Chain D 1–431（431 aa） Fragment：CATALYTIC DOMAIN (1 - 181 & 352 - 402)
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；50 MM TRIS/HCL (PH 6.8), 6 MM MGCL2, 5% MPD, 15% PEG-6K
Resolution 2.80 Å R-free 0.269
1K0U Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue D-eritadenine Deposited 2001-09-20 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 1–431（431 aa）
Chain B 1–431（431 aa）
Chain C 1–431（431 aa）
Chain D 1–431（431 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 DEA D-ERITADENINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.00 Å R-free 0.265
1K0U Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue D-eritadenine Deposited 2001-09-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–431（431 aa）
Chain F 1–431（431 aa）
Chain G 1–431（431 aa）
Chain H 1–431（431 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 DEA D-ERITADENINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.00 Å R-free 0.265
1KY4 S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints Deposited 2002-02-03 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 1–431（431 aa）
Chain B 1–431（431 aa）
Chain C 1–431（431 aa）
Chain D 1–431（431 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.80 Å R-free 0.278
1KY5 D244E mutant S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints Deposited 2002-02-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–431（431 aa）
Chain B 1–431（431 aa）
Chain C 1–431（431 aa）
Chain D 1–431（431 aa）
Mutation：D244E Mutation：D244E Mutation：D244E Mutation：D244E NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 ADY 3'-OXO-ADENOSINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；297 K；PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.80 Å R-free 0.293
1XWF K185N mutated S-adenosylhomocysteine hydrolase Deposited 2004-11-01 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–431（431 aa）
Chain B 1–431（431 aa）
Chain C 1–431（431 aa）
Chain D 1–431（431 aa）
Mutation：K185N Mutation：K185N Mutation：K185N Mutation：K185N NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ADN ADENOSINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；PEG4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.286
2H5L S-Adenosylhomocysteine hydrolase containing NAD and 3-deaza-D-eritadenine Deposited 2006-05-26 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 1–431（431 aa）
Chain B 1–431（431 aa）
Chain C 1–431（431 aa）
Chain D 1–431（431 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 3DD (2R,3R)-4-(4-AMINO-1H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-2,3-DIHYDROXYBUTANOIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；295 K；15% PGE-8000, 50 mM MES, 2% glycerol, pH 6.5, VAPOR DIFFUSION, temperature 295K
Resolution 2.80 Å R-free 0.283
2H5L S-Adenosylhomocysteine hydrolase containing NAD and 3-deaza-D-eritadenine Deposited 2006-05-26 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 1–431（431 aa）
Chain F 1–431（431 aa）
Chain G 1–431（431 aa）
Chain H 1–431（431 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 3DD (2R,3R)-4-(4-AMINO-1H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-2,3-DIHYDROXYBUTANOIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；295 K；15% PGE-8000, 50 mM MES, 2% glycerol, pH 6.5, VAPOR DIFFUSION, temperature 295K
Resolution 2.80 Å R-free 0.283

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SAHH_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–431； UniProt 1–431 Author chain B； PDBConstruct 1–431； UniProt 1–431 Author chain C； PDBConstruct 1–431； UniProt 1–431 Author chain D； PDBConstruct 1–431； UniProt 1–431

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 1d4f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d4f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d4f
Deposition date deposition_date2000-06-22
Structure title titleCRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE
Keywords keywordsS-adenosylhomocysteine hydrolase, AdoHcyase, AdoHcy, Mutagenesis, X-ray crystal structure, Enzyme structure, 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_guinier34.88 Å
Radius of gyration Rg (electron density) rg_electron34.42 Å
Forward intensity I(0) i0565107000.00
Molecular weight molecular_weight193090.0 kDa
Excluded volume excluded_volume241630 ų
Envelope volume envelope_volume278640 ų
Hydration-shell volume shell_volume63729 ų
Envelope diameter envelope_diameter124.5 Å
Shell Rg shell_rg43.46 Å
Envelope Rg envelope_rg34.60 Å
Shape Rg shape_rg34.46 Å
Total Rg total_rg34.86 Å
Total atoms total_atoms13532
Residues n_residues1720
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 dmax112.5 Å
Rg (real space) rg_real34.71 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real5.6510e+08
I(0) uncertainty (real space) i0_real_error9.5980e+06
Rg (reciprocal space) rg_reciprocal34.82 Å
I(0) (reciprocal space) i0_reciprocal565200000.0000
Solution quality estimate total_estimate0.8867
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.0 Å
Skewness Skewness skewness0.198
Kurtosis Kurtosis kurtosis-0.385
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha375500000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.953
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1d4fa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain
Domain ID domain_idd1d4fa2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
Family Family familyc.23.12.3 — S-adenosylhomocystein hydrolase
Domain ID domain_idd1d4fb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain
Domain ID domain_idd1d4fb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
Family Family familyc.23.12.3 — S-adenosylhomocystein hydrolase
Domain ID domain_idd1d4fc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain
Domain ID domain_idd1d4fc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
Family Family familyc.23.12.3 — S-adenosylhomocystein hydrolase
Domain ID domain_idd1d4fd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain
Domain ID domain_idd1d4fd2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
Family Family familyc.23.12.3 — S-adenosylhomocystein hydrolase

CATH v4.4 (8 domains)

Domain ID domain_id1d4fA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1480 — Adenosylhomocysteinase-like
Domain ID domain_id1d4fA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1d4fB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1480 — Adenosylhomocysteinase-like
Domain ID domain_id1d4fB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1d4fC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1480 — Adenosylhomocysteinase-like
Domain ID domain_id1d4fC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1d4fD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1480 — Adenosylhomocysteinase-like
Domain ID domain_id1d4fD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
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8. Citations (1)

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9. Files and Curves (10)