2b83

A single amino acid substitution in the Clostridium beijerinckii alcohol dehydrogenase is critical for thermostabilization

Method: X-RAY DIFFRACTION D_max: 93.0 Å Quality: GOOD

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

NADP-dependent alcohol dehydrogenase

Clostridium beijerinckii

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 1–351 Chain B； UniProt 1–351 Chain C； UniProt 1–351 Chain D； UniProt 1–351	Mutation：Q100P	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 6；298 K；5% PEG 100; 30% PEG600; 10% Glycerol; MES 0.1M, Microbatch, temperature 298K	Resolution 2.25 Å R-free 0.230

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 2B83	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JQB Alcohol Dehydrogenase from Clostridium Beijerinckii: Crystal Structure of Mutant with Enhanced Thermal Stability Deposited 2001-08-05	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–351（351 aa） Chain B 1–351（351 aa） Chain C 1–351（351 aa） Chain D 1–351（351 aa）	Mutation：Q165E,M304R,V224E,S254K Mutation：Q165E,M304R,V224E,S254K Mutation：Q165E,M304R,V224E,S254K Mutation：Q165E,M304R,V224E,S254K	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；292 K；PEG 4000, Tris-Cl, NaCl, NADP, ZnCl2, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K	Resolution 1.97 Å R-free 0.247
1KEV STRUCTURE OF NADP-DEPENDENT ALCOHOL DEHYDROGENASE Deposited 1996-10-21	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 1–351（351 aa） Chain B 1–351（351 aa） Chain C 1–351（351 aa） Chain D 1–351（351 aa）	Not recorded	ZN ZINC ION × 4 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；SEE REFERENCE 1, pH 8.2	Resolution 2.05 Å R-free 0.259
1PED BACTERIAL SECONDARY ALCOHOL DEHYDROGENASE (APO-FORM) Deposited 1995-12-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–351（351 aa） Chain B 1–351（351 aa） Chain C 1–351（351 aa） Chain D 1–351（351 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；SEE REFERENCE 1., pH 7.5	Resolution 2.15 Å R-free 0.258
3FPL Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of C. beijerinckii ADH by T. brockii 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 1–152（152 aa） Chain A 296–351（56 aa）	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 8 EDO 1,2-ETHANEDIOL × 4 CAC CACODYLATE ION × 4 PGE TRIETHYLENE GLYCOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；298 K；Single crystals of apo-22(CTC) were obtained by the microbatch method under oil at 18 C, using the IMPAX 1-5 robot. The apo-22(CTC) (10mg/mL) was crystallized in a mixture containing 100mM ammonium acetate, 15% (w/v) PEG 4000, 25mM NaCl, 50mM DTT, 25mM ZnCl2 and 50mM tri-citrate dihydrate (pH sodium 5.6), Microbatch, temperature 298K	Resolution 1.90 Å R-free 0.172
3FSR Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of T. brockii ADH by C. beijerinckii ADH Deposited 2009-01-11	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 153–295（143 aa） Chain B 153–295（143 aa） Chain C 153–295（143 aa） Chain D 153–295（143 aa）	Not recorded	ZN ZINC ION × 6 EDO 1,2-ETHANEDIOL × 5 CL CHLORIDE ION × 1	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 0.001ml 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 2.20 Å R-free 0.220
3FTN Q165E/S254K Double Mutant Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of T. brockii ADH by C. beijerinckii ADH Deposited 2009-01-13	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 153–295（143 aa） Chain B 153–295（143 aa） Chain C 153–295（143 aa） Chain D 153–295（143 aa）	Mutation：Q165E, S254K Mutation：Q165E, S254K Mutation：Q165E, S254K Mutation：Q165E, S254K	ZN ZINC ION × 4 ACT ACETATE ION × 4 EDO 1,2-ETHANEDIOL × 11 CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8 mg/mL protein, 25 mM Tris-HCl, 50 mM NaCl, 0.1 mM DTT, 50 mM ZnCl2 (pH=7.5)] was mixed with 1 microliter of reservoir solution [16% (w/v) PEG8K, 200 mM magnesium acetate tetrahydrate, 100 mM Cacodylate buffer (pH 6.5), vapor diffusion, hanging drop, temperature 298K	Resolution 2.19 Å R-free 0.228
6SCH NADH-dependent variant of CBADH Deposited 2019-07-24	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 1–351（351 aa） Chain B 1–351（351 aa） Chain C 1–351（351 aa） Chain D 1–351（351 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 2PE NONAETHYLENE GLYCOL × 8 ZN ZINC ION × 4 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；290 K；900 mM sodium citrate, 100 mM imidazole pH 8	Resolution 2.20 Å R-free 0.208

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ADH_CLOBE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–351； UniProt 1–351 Author chain B； PDBConstruct 1–351； UniProt 1–351 Author chain C； PDBConstruct 1–351； UniProt 1–351 Author chain D； PDBConstruct 1–351； UniProt 1–351

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2b83
Deposition date deposition_date	2005-10-06
Structure title title	A single amino acid substitution in the Clostridium beijerinckii alcohol dehydrogenase is critical for thermostabilization
Keywords keywords	CbADH MUTANT, Metal binding, Structural Genomics, Israel Structural Proteomics Center, ISPC, OXIDOREDUCTASE; 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	32.64 Å
Radius of gyration Rg (electron density) rg_electron	32.04 Å
Forward intensity I(0) i0	345958000.00
Molecular weight molecular_weight	150990.0 kDa
Excluded volume excluded_volume	189620 Å³
Envelope volume envelope_volume	224680 Å³
Hydration-shell volume shell_volume	55727 Å³
Envelope diameter envelope_diameter	99.4 Å
Shell Rg shell_rg	41.07 Å
Envelope Rg envelope_rg	31.93 Å
Shape Rg shape_rg	32.08 Å
Total Rg total_rg	32.55 Å
Total atoms total_atoms	10556
Residues n_residues	1404
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	93.0 Å
Rg (real space) rg_real	32.37 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	3.4600e+08
I(0) uncertainty (real space) i0_real_error	4.8710e+06
Rg (reciprocal space) rg_reciprocal	32.49 Å
I(0) (reciprocal space) i0_reciprocal	346000000.0000
Solution quality estimate total_estimate	0.8896
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.7 Å
Skewness Skewness skewness	0.077
Kurtosis Kurtosis kurtosis	-0.558
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	181900000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.981; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.640

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	NADP-dependent alcohol dehydrogenase
Molecular weight formula_weight	37731.9 kDa
EC 编号 ec_number	1.1.1.2
Mutation mutation	Q100P
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	11080

MKGFAMLGINKLGWIEKERPVAGSYDAIVRPLAVSPCTSDIHTVFEGALGDRKNMILGHEAVGEVVEVGSEVKDFKPGDRVIVPCTTPDWRSLEVQAGFPQHSNGMLAGWKFSNFKDGVFGEYFHVNDADMNLAILPKDMPLENAVMITDMMTTGFHGAELADIQMGSSVVVIGIGAVGLMGIAGAKLRGAGRIIGVGSRPICVEAAKFYGATDILNYKNGHIVDQVMKLTNGKGVDRVIMAGGGSETLSQAVSMVKPGGIISNINYHGSGDALLIPRVEWGCGMAHKTIKGGLCPGGRLRAEMLRDMVVYNRVDLSKLVTHVYHGFDHIEEALLLMKDKPKDLIKAVVIL

来源 Source

来源生物 organism	Clostridium beijerinckii
NCBI Class编号 ncbi_taxonomy_id	1520
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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	524

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2b83a1
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d2b83a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

Domain ID domain_id	d2b83b1
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d2b83b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

Domain ID domain_id	d2b83c1
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d2b83c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

Domain ID domain_id	d2b83d1
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d2b83d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	2b83A01
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	2b83A02
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	2b83B01
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	2b83B02
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	2b83C01
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	2b83C02
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	2b83D01
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	2b83D02
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	79.470 Å
Unit-cell length b length_b	103.340 Å
Unit-cell length c length_c	193.307 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	39.530 Å
R factor r_factor	0.2290
R_work r_work	0.1930
R_free r_free	0.2300

fit	/app/data/saxs_computation/b8/2b83/2b83.fit
pddf	/app/data/pr_computation/b8/2b83/2b83.pr.out
profile	/app/data/saxs_computation/b8/2b83/2b83.dat