SAXSdb — 1gjp

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

5-AMINOLAEVULINIC ACID DEHYDRATASE

SACCHAROMYCES CEREVISIAE

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 1–340	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

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 1GJP	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 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 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
1H7N SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH LAEVULINIC ACID AT 1.6 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 1–342（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 construct 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 construct 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 construct 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 construct 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 construct 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
1W31 YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 5-HYDROXYLAEVULINIC ACID COMPLEX Deposited 2004-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–342（342 aa）	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
1YLV SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH LAEVULINIC ACID Deposited 1999-02-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–342（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 1–340； UniProt 1–340

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	1gjp
Deposition date deposition_date	2001-08-01
Structure title title	SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH 4-OXOSEBACIC ACID
Keywords keywords	LYASE, DEHYDRATASE, ALDOLASE, TIM BARREL, TETRAPYRROLE SYNTHESIS; DEHYDRATASE
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	22.99 Å
Radius of gyration Rg (electron density) rg_electron	22.18 Å
Forward intensity I(0) i0	24156700.00
Molecular weight molecular_weight	37740.0 kDa
Excluded volume excluded_volume	47336 Å³
Envelope volume envelope_volume	61802 Å³
Hydration-shell volume shell_volume	23413 Å³
Envelope diameter envelope_diameter	92.6 Å
Shell Rg shell_rg	28.38 Å
Envelope Rg envelope_rg	25.50 Å
Shape Rg shape_rg	22.19 Å
Total Rg total_rg	22.95 Å
Total atoms total_atoms	2652
Residues n_residues	340
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	89.4 Å
Rg (real space) rg_real	23.32 Å
Rg uncertainty (real space) rg_real_error	1.03 Å
I(0) (real space) i0_real	2.4160e+07
I(0) uncertainty (real space) i0_real_error	4.1550e+05
Rg (reciprocal space) rg_reciprocal	23.24 Å
I(0) (reciprocal space) i0_reciprocal	24160000.0000
Solution quality estimate total_estimate	0.7477
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.944
Kurtosis Kurtosis kurtosis	1.180
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6611000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.332; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.743; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	5-AMINOLAEVULINIC ACID DEHYDRATASE
Molecular weight formula_weight	37541.9 kDa
EC 编号 ec_number	4.2.1.24
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3159

MHTAEFLETEPTEISSVLAGGYNHPLLRQWQSERQLTKNMLIFPLFISDNPDDFTEIDSLPNINRIGVNRLKDYLKPLVAKGLRSVILFGVPLIPGTKDPVGTAADDPAGPVIQGIKFIREYFPELYIICDVCLCEYTSHGHCGVLYDDGTINRERSVSRLAAVAVNYAKAGAHCVAPSDMIDGRIRDIKRGLINANLAHKTFVLSYAAKFSGNLYGPFRDAACSAPSNGDRKCYQLPPAGRGLARRALERDMSEGADGIIVKPSTFYLDIMRDASEICKDLPICAYHVSGEYAMLHAAAEKGVVDLKTIAFESHQGFLRAGARLIITYLAPEFLDWLDE

来源 Source

来源生物 organism	SACCHAROMYCES CEREVISIAE
通用名 common_name	;BAKER'S YEAST ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	4-OXODECANEDIOIC ACID
Molecular weight formula_weight	216.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	465

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1gjpa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.3 — 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)

CATH v4.4 (1 domains)

Domain ID domain_id	1gjpA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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8. Citations (1)

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Unit-cell length a length_a	103.500 Å
Unit-cell length b length_b	103.500 Å
Unit-cell length c length_c	168.200 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	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	30.400 Å
R factor r_factor	0.2650
R_work r_work	—
R_free r_free	0.3290

fit	/app/data/saxs_computation/gj/1gjp/1gjp.fit
pddf	/app/data/pr_computation/gj/1gjp/1gjp.pr.out
profile	/app/data/saxs_computation/gj/1gjp/1gjp.dat

SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH 4-OXOSEBACIC ACID

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

5-AMINOLAEVULINIC ACID DEHYDRATASE

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