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1w31

YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 5-HYDROXYLAEVULINIC ACID COMPLEX

Method: X-RAY DIFFRACTION Dmax: 89.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DELTA-AMINOLEVULINIC ACID DEHYDRATASE

SACCHAROMYCES CEREVISIAE

UniProt P05373

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–342 Not recorded SHO 5-HYDROXYLAEVULINIC ACID × 8 ZN ZINC ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；ENZYME CONCENTRATION 1 MG/ML, PH 7.0 - 8.5, BUFFER 0.2 M TRIS-HCL, PRECIPITANT PEG 6000 (<10%), 70 MICROMOLAR ZINC SULPHATE, 6 MM BETA-MERCAPTOETHANOL, HANGING DROPS AS FOR PDB ENTRY 1AW5 WITH 10 MM 5-HYDROXYLAEVULINIC ACID IN DROP. Resolution 1.90 Å R-free 0.249

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 1W31 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AW5 5-AMINOLEVULINATE DEHYDRATASE FROM SACCHAROMYCES CEREVISIAE Deposited 1997-10-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–340（340 aa）
Mutation：M272V Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；ENZYME CONCENTRATION 1 MG/ML, PH 7.0 - 8.5, BUFFER 0.2 M TRIS-HCL, PRECIPITANT PEG 6000 (<10%), 70 MICROMOLAR ZINC SULPHATE, 6 MM BETA-MERCAPTOETHANOL, HANGING DROPS., pH 8.0, vapor diffusion - hanging drop
Resolution 2.30 Å R-free 0.270
1EB3 YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 4,7-DIOXOSEBACIC ACID COMPLEX Deposited 2001-07-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–340（340 aa）
Not recorded DSB 4,7-DIOXOSEBACIC ACID × 8 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；AS FOR PDB ENTRY 1AW5 WITH 5 MM 4,7-DIOXO-SEBACIC ACID IN DROP, pH 8.00
Resolution 1.75 Å R-free 0.308
1GJP SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH 4-OXOSEBACIC ACID Deposited 2001-08-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–340（340 aa）
Not recorded 4OX 4-OXODECANEDIOIC ACID × 8 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；AS FOR 1AW5 WITH 5MM 4-OXOSEBACIC ACID IN DROP, pH 8.00
Resolution 1.80 Å R-free 0.329
1H7N SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH LAEVULINIC ACID AT 1.6 A RESOLUTION Deposited 2001-07-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–342（342 aa）
Not recorded SHF LAEVULINIC ACID × 8 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；AS FOR 1AW5 WITH 10MM LAEVULINIC ACID, pH 8.00
Resolution 1.60 Å R-free 0.265
1H7O SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH 5-AMINOLAEVULINIC ACID AT 1.7 A RESOLUTION Deposited 2001-07-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–341（341 aa）
Not recorded DAV DELTA-AMINO VALERIC ACID × 8 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；AS FOR 1AW5, EXCEPT ENZYME WAS NOT GEL-FILTERED., pH 8.00
Resolution 1.75 Å R-free 0.353
1H7P SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH 4-KETO-5-AMINO-HEXANOIC (KAH) AT 1.64 A RESOLUTION Deposited 2001-07-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–342（342 aa）
Not recorded KAH 5-AMINO-4-HYDROXYHEXANOIC ACID × 8 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；AS FOR 1AW5 WITH 1MM KAH PRESENT., pH 8.00
Resolution 1.64 Å R-free 0.301
1H7R SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH SUCCINYLACETONE AT 2.0 A RESOLUTION. Deposited 2001-07-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–342（342 aa）
Not recorded SHU 4,6-DIOXOHEPTANOIC ACID × 8 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；AS FOR 1AW5 WITH 6MM SUCCINYLACETONE PRESENT., pH 8.00
Resolution 2.00 Å R-free 0.310
1OHL YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE PUTATIVE CYCLIC REACTION INTERMEDIATE COMPLEX Deposited 2003-05-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–342（342 aa）
Not recorded ZN ZINC ION × 8 BME BETA-MERCAPTOETHANOL × 8 PBG 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；AS FOR PDB ENTRY 1AW5, pH 8.00
Resolution 1.60 Å R-free 0.241
1QML Hg complex of yeast 5-aminolaevulinic acid dehydratase Deposited 1999-10-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–342（342 aa）
Not recorded HG MERCURY (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；AS FOR 1AW5 WITH 1MM HGCL, pH 8.00
Resolution 3.00 Å R-free 0.330
1QNV yeast 5-aminolaevulinic acid dehydratase Lead (Pb) complex Deposited 1999-10-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–342（342 aa）
Not recorded PB LEAD (II) ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；AS FOR PDB ENTRY 1AW5 WITH 1MM LEAD ACETATE, pH 8.00
Resolution 2.50 Å R-free 0.379
1YLV SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH LAEVULINIC ACID Deposited 1999-02-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–342（342 aa）
Not recorded ZN ZINC ION × 8 SHF LAEVULINIC ACID × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；AS FOR 1AW5 WITH 10MM LAEVULINIC ACID, pH 8.0
Resolution 2.15 Å R-free 0.265

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HEM2_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–342； UniProt 1–342

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 1w31

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1w31
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1w31
Deposition date deposition_date2004-07-11
Structure title titleYEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 5-HYDROXYLAEVULINIC ACID COMPLEX
Keywords keywordsDEHYDRATASE, ALDOLASE, TIM BARREL, TETRAPYRROLE SYNTHESIS, HEME BIOSYNTHESIS, LYASE, ZINC; LYASE
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_guinier22.92 Å
Radius of gyration Rg (electron density) rg_electron22.16 Å
Forward intensity I(0) i024096000.00
Molecular weight molecular_weight37658.0 kDa
Excluded volume excluded_volume47215 ų
Envelope volume envelope_volume61274 ų
Hydration-shell volume shell_volume23263 ų
Envelope diameter envelope_diameter92.5 Å
Shell Rg shell_rg28.26 Å
Envelope Rg envelope_rg25.55 Å
Shape Rg shape_rg22.17 Å
Total Rg total_rg22.91 Å
Total atoms total_atoms2646
Residues n_residues340
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 dmax89.1 Å
Rg (real space) rg_real23.25 Å
Rg uncertainty (real space) rg_real_error0.90 Å
I(0) (real space) i0_real2.4100e+07
I(0) uncertainty (real space) i0_real_error3.4760e+05
Rg (reciprocal space) rg_reciprocal23.17 Å
I(0) (reciprocal space) i0_reciprocal24090000.0000
Solution quality estimate total_estimate0.7457
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.0 Å
Skewness Skewness skewness0.955
Kurtosis Kurtosis kurtosis1.211
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6172000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.328; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.740; Smooth: 0.965
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1w31a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.10 — Aldolase
Family Family familyc.1.10.3 — 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)

CATH v4.4 (1 domains)

Domain ID domain_id1w31A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
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8. Citations (1)

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9. Files and Curves (10)