SAXSdb — 1bdb

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

CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE

OrganismNot specified

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 1–277	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 0.1 M CITRATE/PHOSPHATE BUFFER, PH 7.5, 1.2 M AMMONIUM SULFATE CONTAINING 50 MM NAD	Resolution 2.00 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	BPHB_BURCE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–277； UniProt 1–277

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	1bdb
Deposition date deposition_date	1997-05-10
Structure title title	CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PSEUDOMONAS SP. LB400
Keywords keywords	NAD-DEPENDENT OXIDOREDUCTASE, SHORT-CHAIN ALCOHOL DEHYDROGENASE, PCB DEGRADATION, 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	19.92 Å
Radius of gyration Rg (electron density) rg_electron	19.00 Å
Forward intensity I(0) i0	14644800.00
Molecular weight molecular_weight	28567.0 kDa
Excluded volume excluded_volume	35701 Å³
Envelope volume envelope_volume	42610 Å³
Hydration-shell volume shell_volume	18994 Å³
Envelope diameter envelope_diameter	70.0 Å
Shell Rg shell_rg	25.35 Å
Envelope Rg envelope_rg	19.99 Å
Shape Rg shape_rg	19.01 Å
Total Rg total_rg	19.90 Å
Total atoms total_atoms	2013
Residues n_residues	267
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	67.1 Å
Rg (real space) rg_real	19.95 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.4640e+07
I(0) uncertainty (real space) i0_real_error	1.8180e+05
Rg (reciprocal space) rg_reciprocal	19.95 Å
I(0) (reciprocal space) i0_reciprocal	14640000.0000
Solution quality estimate total_estimate	0.7806
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.462
Kurtosis Kurtosis kurtosis	0.004
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2778000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.729; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.000

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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	CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE
Molecular weight formula_weight	28929.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2133

MKLKGEAVLITGGASGLGRALVDRFVAEGAKVAVLDKSAERLAELETDHGDNVLGIVGDVRSLEDQKQAASRCVARFGKIDTLIPNAGIWDYSTALVDLPEESLDAAFDEVFHINVKGYIHAVKACLPALVASRGNVIFTISNAGFYPNGGGPLYTAAKHAIVGLVRELAFELAPYVRVNGVGSGGINSDLRGPSSLGMGSKAISTVPLADMLKSVLPIGRMPEVEEYTGAYVFFATRGDAAPATGALLNYDGGLGVRGFFSGAGGNDLLEQLNIHP

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bdba_
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.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (1 domains)

Domain ID domain_id	1bdbA00
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 (2)

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Unit-cell length a length_a	79.200 Å
Unit-cell length b length_b	79.200 Å
Unit-cell length c length_c	152.880 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.1790
R_free r_free	0.2300

fit	/app/data/saxs_computation/bd/1bdb/1bdb.fit
pddf	/app/data/pr_computation/bd/1bdb/1bdb.pr.out
profile	/app/data/saxs_computation/bd/1bdb/1bdb.dat

CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PSEUDOMONAS SP. LB400

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

CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE

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