SAXSdb — 2oui

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

NADP-dependent alcohol dehydrogenase

Entamoeba histolytica

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 1–360 Chain B； UniProt 1–360 Chain C； UniProt 1–360 Chain D； UniProt 1–360	Mutation：D275P	ZN ZINC ION × 4 NO3 NITRATE ION × 4 CAC CACODYLATE ION × 4 EDO 1,2-ETHANEDIOL × 9 PGE TRIETHYLENE GLYCOL × 4 1PE PENTAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；8mg/mL protein, 25mM Tris-HCl, 50mM NaCl, 0.1mM DTT, 50mM ZnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.77 Å R-free 0.178

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 2OUI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y9A Alcohol Dehydrogenase from Entamoeba histolotica in complex with cacodylate Deposited 2004-12-15	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 1–360（360 aa） Chain C 1–360（360 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 8 CAC CACODYLATE ION × 4 ACT ACETATE ION × 4 MG MAGNESIUM ION × 4 EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 8000 14%w/v, 300 mM Mg Acetate, 200mM cacodylate at pH 6.5, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.81 Å R-free 0.177
3FPC Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica ADH Deposited 2009-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 153–294（142 aa） Chain B 153–294（142 aa） Chain C 153–294（142 aa） Chain D 153–294（142 aa）	Not recorded	ZN ZINC ION × 4 CAC CACODYLATE ION × 4 OXY OXYGEN MOLECULE × 1 EDO 1,2-ETHANEDIOL × 14 NO3 NITRATE ION × 2 IMD IMIDAZOLE × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8mg/mL protein [25mM Tris-HCl, 50mM NaCl, 0.1mM DTT, 50mM ZnCl2 (pH=7.5)] was mixed with 0.001 ml of reservoir solution [16% (w/v) PEG 8000, 200mM magnesium acetate tetrahydrate, 100mM Cacodylate buffer (pH 6.5)], vapor diffusion, hanging drop, temperature 298K	Resolution 1.40 Å R-free 0.155

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ADH1_ENTHI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–360； UniProt 1–360 Author chain B； PDBConstruct 1–360； UniProt 1–360 Author chain C； PDBConstruct 1–360； UniProt 1–360 Author chain D； PDBConstruct 1–360； UniProt 1–360

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	2oui
Deposition date deposition_date	2007-02-11
Structure title title	D275P mutant of alcohol dehydrogenase from protozoa Entamoeba histolytica
Keywords keywords	Tetramer, METAL-BINDING, NADP, OXIDOREDUCTASE, P275D MUTATION, cacodylate ion, thermosatbility; OXIDOREDUCTASE
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	33.08 Å
Radius of gyration Rg (electron density) rg_electron	32.33 Å
Forward intensity I(0) i0	378967000.00
Molecular weight molecular_weight	156860.0 kDa
Excluded volume excluded_volume	196410 Å³
Envelope volume envelope_volume	233350 Å³
Hydration-shell volume shell_volume	56986 Å³
Envelope diameter envelope_diameter	107.3 Å
Shell Rg shell_rg	41.50 Å
Envelope Rg envelope_rg	32.44 Å
Shape Rg shape_rg	32.34 Å
Total Rg total_rg	32.95 Å
Total atoms total_atoms	10962
Residues n_residues	1440
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	98.9 Å
Rg (real space) rg_real	32.81 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	3.7900e+08
I(0) uncertainty (real space) i0_real_error	5.2850e+06
Rg (reciprocal space) rg_reciprocal	32.93 Å
I(0) (reciprocal space) i0_reciprocal	379000000.0000
Solution quality estimate total_estimate	0.9015
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.3 Å
Skewness Skewness skewness	0.100
Kurtosis Kurtosis kurtosis	-0.519
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	175800000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.901

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	NADP-dependent alcohol dehydrogenase
Molecular weight formula_weight	38603.6 kDa
EC 编号 ec_number	1.1.1.2
Mutation mutation	D275P
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12226

MKGLAMLGIGRIGWIEKKIPECGPLDALVRPLALAPCTSDTHTVWAGAIGDRHDMILGHEAVGQIVKVGSLVKRLKVGDKVIVPAITPDWGEEESQRGYPMHSGGMLGGWKFSNFKDGVFSEVFHVNEADANLALLPRDIKPEDAVMLSDMVTTGFHGAELANIKLGDTVCVIGIGPVGLMSVAGANHLGAGRIFAVGSRKHCCDIALEYGATDIINYKNGDIVEQILKATDGKGVDKVVIAGGDVHTFAQAVKMIKPGSDIGNVNYLGEGDNIPIPRSEWGVGMGHKHIHGGLTPGGRVRMEKLASLISTGKLDTSKLITHRFEGLEKVEDALMLMKNKPADLIKPVVRIHYDDEDTLH

来源 Source

来源生物 organism	Entamoeba histolytica
NCBI Class编号 ncbi_taxonomy_id	5759
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 6 Entity 6 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1075

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2ouiA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	2ouiA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2ouiB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	2ouiB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2ouiC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	2ouiC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2ouiD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	2ouiD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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8. Citations (1)

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Unit-cell length a length_a	145.921 Å
Unit-cell length b length_b	144.104 Å
Unit-cell length c length_c	80.073 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	121.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.770 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1496
R_work r_work	0.1481
R_free r_free	0.1779

fit	/app/data/saxs_computation/ou/2oui/2oui.fit
pddf	/app/data/pr_computation/ou/2oui/2oui.pr.out
profile	/app/data/saxs_computation/ou/2oui/2oui.dat

D275P mutant of alcohol dehydrogenase from protozoa Entamoeba histolytica