SAXSdb — 1b7g

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

PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE)

Sulfolobus solfataricus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain O； UniProt 1–341 Chain Q； UniProt 1–341	Mutation：YES	SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 2.05 Å R-free 0.293
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain O； UniProt 1–341 Chain Q； UniProt 1–341	Mutation：YES	SO4 SULFATE ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 2.05 Å R-free 0.293

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	G3P_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain O； PDBConstruct 1–340； UniProt 1–341 Author chain Q； PDBConstruct 1–340； UniProt 1–341

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	1b7g
Deposition date deposition_date	1999-01-22
Structure title title	GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
Keywords keywords	ARCHAEA; HYPERTHERMOPHILE; GAPDH; HYPERTHERMOPHILIC DEHYDROGENASE, 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	28.00 Å
Radius of gyration Rg (electron density) rg_electron	27.29 Å
Forward intensity I(0) i0	95391200.00
Molecular weight molecular_weight	76322.0 kDa
Excluded volume excluded_volume	95651 Å³
Envelope volume envelope_volume	113510 Å³
Hydration-shell volume shell_volume	34262 Å³
Envelope diameter envelope_diameter	93.2 Å
Shell Rg shell_rg	35.14 Å
Envelope Rg envelope_rg	27.38 Å
Shape Rg shape_rg	27.28 Å
Total Rg total_rg	28.10 Å
Total atoms total_atoms	5328
Residues n_residues	680
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	88.2 Å
Rg (real space) rg_real	27.94 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	9.5390e+07
I(0) uncertainty (real space) i0_real_error	1.4090e+06
Rg (reciprocal space) rg_reciprocal	27.96 Å
I(0) (reciprocal space) i0_reciprocal	95390000.0000
Solution quality estimate total_estimate	0.9063
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.9 Å
Skewness Skewness skewness	0.262
Kurtosis Kurtosis kurtosis	-0.552
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29070000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.974

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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	PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE)
Molecular weight formula_weight	37631.6 kDa
EC 编号 ec_number	1.2.1.12
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,Q
Atom count atom_count	5844

MVNVAVNGYGTIGKRVADAIIKQPDMKLVGVAKTSPNYEAFIAHRRGIRIYVPQQSIKKFEESGIPVAGTVEDLIKTSDIVVDTTPNGVGAQYKPIYLQLQRNAIFQGGEKAEVADISFSALCNYNEALGKKYIRVVSCNTTALLRTICTVNKVSKVEKVRATIVRRAADQKEVKKGPINSLVPDPATVPSHHAKDVNSVIRNLDIATMAVIAPTTLMHMHFINITLKDKVEKKDILSVLENTPRIVLISSKYDAEATAELVEVARDLKRDRNDIPEVMIFSDSIYVKDDEVMLMYAVHQESIVVPENIDAIRASMKLMSAEDSMRITNESLGILKGYLI

来源 Source

来源生物 organism	Sulfolobus solfataricus
NCBI Class编号 ncbi_taxonomy_id	2287
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	516

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1b7go1
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.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1b7go2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d1b7gq1
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.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1b7gq2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

CATH v4.4 (4 domains)

Domain ID domain_id	1b7gO01
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	1b7gO02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	1b7gQ01
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	1b7gQ02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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8. Citations (2)

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Unit-cell length a length_a	101.550 Å
Unit-cell length b length_b	101.550 Å
Unit-cell length c length_c	179.920 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	22.000 Å
R factor r_factor	—
R_work r_work	0.2260
R_free r_free	0.2930

fit	/app/data/saxs_computation/b7/1b7g/1b7g.fit
pddf	/app/data/pr_computation/b7/1b7g/1b7g.pr.out
profile	/app/data/saxs_computation/b7/1b7g/1b7g.dat

GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE

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

PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE 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