SAXSdb — 1dgj

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

ALDEHYDE OXIDOREDUCTASE

Desulfovibrio desulfuricans

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–907	Not recorded	FES FE2/S2 (INORGANIC) CLUSTER × 2 2MO MOLYBDENUM (IV)OXIDE × 1 MCN PTERIN CYTOSINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；ammonium sulphate, MES, dioxane, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.80 Å R-free 0.224

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	Q9REC4_DESDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–907； UniProt 1–907

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	1dgj
Deposition date deposition_date	1999-11-24
Structure title title	CRYSTAL STRUCTURE OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774
Keywords keywords	BETA HALF-BARREL, FOUR-HELIX BUNDLE, BETA BARREL, 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	28.13 Å
Radius of gyration Rg (electron density) rg_electron	27.33 Å
Forward intensity I(0) i0	163885000.00
Molecular weight molecular_weight	98887.0 kDa
Excluded volume excluded_volume	122600 Å³
Envelope volume envelope_volume	142960 Å³
Hydration-shell volume shell_volume	41484 Å³
Envelope diameter envelope_diameter	95.0 Å
Shell Rg shell_rg	36.33 Å
Envelope Rg envelope_rg	27.84 Å
Shape Rg shape_rg	27.33 Å
Total Rg total_rg	28.12 Å
Total atoms total_atoms	6909
Residues n_residues	906
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	89.6 Å
Rg (real space) rg_real	27.95 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.6390e+08
I(0) uncertainty (real space) i0_real_error	2.3920e+06
Rg (reciprocal space) rg_reciprocal	28.01 Å
I(0) (reciprocal space) i0_reciprocal	163900000.0000
Solution quality estimate total_estimate	0.8960
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.183
Kurtosis Kurtosis kurtosis	-0.451
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42890000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	ALDEHYDE OXIDOREDUCTASE
Molecular weight formula_weight	98017.8 kDa
EC 编号 ec_number	1.2.-.-
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	7102

METKTLIVNGMARRLLVSPNDLLVDVLRSQLQLTSVKVGCGKGQCGACTVILDGKVVRACIIKMSRVAENASVTTLEGIGAPDCLHPLQHAWIQHGAAQCGFCTPGFIVSAKALLDENVAPSREDVRDWFQKHHNICRCTGYKPLVDAVMDAAAILRGEKTVEEISFKMPADGRIWGSSIPRPSAVAKVTGLAEFGADAALRMPENTLHLALAQAKVSHALIKGIDTSEAEKMPGVYKVLTHKDVKGKNRITGLITFPTNKGDGWERPILNDSKIFQYGDALAIVCADSEANARAAAEKVKFDLELLPEYMSAPEAMAPDAIEIHPGTPNVYYDQLEEKGEDTVPFFNDPANVVAEGSYYTQRQPHLPIEPDVGYGYINEQGQVVIHSKSVAIHLHALMIAPGLGLEFPKDLVLVQNTTGGTFGYKFSPTMEALVGVAVMATGRPCHLRYNYEQQQNYTGKRSPFWTTMRYAADRQGKILAMETDWSVDHGPYSEFGDLLTLRGAQYIGAGYGIANIRGTGRTVATNHCWGAAFRGYGAPESEFPSEVLMDELAEKLGMDPFELRALNCYREGDTTSSGQIPEVMSLPEMFDKMRPYYEESKKRVKERSTAEIKRGVGVALGVYGAGLDGPDTSEAWVELNDDGSVTLGNSWEDHGQGADAGSLGTAHEALRPLGITPENIHLVMNDTSKTPNSGPAGGSRSQVVTGNAIRVACEMLIEGMRKPGGGFFTPAEMKAEGRPMRYDGKWTAPAKDCDAKGQGSPFACYMYGLFLTEVAVEVATGKATVEKMVCVADIGKICNKLVVDGQIYGGLAQGVGLALSEDYEDLKKHSTMGGAGIPSIKMIPDDIEIVYVETPRKDGPFGASGVGEMPLTAPHAAIINGIYNACGARVRHLPARPEKVLEAMPR

来源 Source

来源生物 organism	Desulfovibrio desulfuricans
NCBI Class编号 ncbi_taxonomy_id	876
宿主生物 host_organism	Bacteria

Entity 2 Entity 2 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MOLYBDENUM (IV)OXIDE
Molecular weight formula_weight	127.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PTERIN CYTOSINE DINUCLEOTIDE
Molecular weight formula_weight	696.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	193

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dgja1
Class class	a — All alpha proteins
Fold Fold fold	a.56 — CO dehydrogenase ISP C-domain like
Superfamily Superfamily superfamily	a.56.1 — CO dehydrogenase ISP C-domain like
Family Family family	a.56.1.1 — CO dehydrogenase ISP C-domain like

Domain ID domain_id	d1dgja2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins

Domain ID domain_id	d1dgja3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.1 — CO dehydrogenase molybdoprotein N-domain-like
Family Family family	d.41.1.1 — CO dehydrogenase molybdoprotein N-domain-like

Domain ID domain_id	d1dgja4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.133 — Molybdenum cofactor-binding domain
Superfamily Superfamily superfamily	d.133.1 — Molybdenum cofactor-binding domain
Family Family family	d.133.1.1 — Molybdenum cofactor-binding domain

CATH v4.4 (7 domains)

Domain ID domain_id	1dgjA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

Domain ID domain_id	1dgjA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	120 — [2Fe-2S]-binding domain

Domain ID domain_id	1dgjA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead

Domain ID domain_id	1dgjA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	1dgjA05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	1dgjA06
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	1dgjA07
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

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8. Citations (1)

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Unit-cell length a length_a	156.639 Å
Unit-cell length b length_b	156.639 Å
Unit-cell length c length_c	177.149 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 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	24.800 Å
R factor r_factor	0.1670
R_work r_work	0.1640
R_free r_free	0.2240

fit	/app/data/saxs_computation/dg/1dgj/1dgj.fit
pddf	/app/data/pr_computation/dg/1dgj/1dgj.pr.out
profile	/app/data/saxs_computation/dg/1dgj/1dgj.dat

CRYSTAL STRUCTURE OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774

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

ALDEHYDE OXIDOREDUCTASE

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