SAXSdb — 1d2t

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

ACID PHOSPHATASE

Escherichia blattae

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 19–249	Fragment：ACID PHOSPHATASE	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG400, TRIS, HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.257

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 1D2T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EOI CRYSTAL STRUCTURE OF ACID PHOSPHATASE FROM ESCHERICHIA BLATTAE COMPLEXED WITH THE TRANSITION STATE ANALOG MOLYBDATE Deposited 2000-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 19–249（231 aa） Chain B 19–249（231 aa） Chain C 19–249（231 aa）	Not recorded	MOO MOLYBDATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；PEG400, Na2MoO4, Tris, Hepes, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 2.40 Å R-free 0.280
1IW8 Crystal Structure of a mutant of acid phosphatase from Escherichia blattae (G74D/I153T) Deposited 2002-04-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 19–249（231 aa） Fragment：residues 1-231 Chain B 19–249（231 aa） Fragment：residues 1-231 Chain C 19–249（231 aa） Fragment：residues 1-231 Chain D 19–249（231 aa） Fragment：residues 1-231 Chain E 19–249（231 aa） Fragment：residues 1-231 Chain F 19–249（231 aa） Fragment：residues 1-231	Mutation：G74D, I153T Mutation：G74D, I153T Mutation：G74D, I153T Mutation：G74D, I153T Mutation：G74D, I153T Mutation：G74D, I153T	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；PEG400, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.284

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

View Construct and Data Evidence

UniProt name	Q9S1A6_ESCBL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–231； UniProt 19–249

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	1d2t
Deposition date deposition_date	1999-09-28
Structure title title	CRYSTAL STRUCTURE OF ACID PHOSPHATASE FROM ESCHERICHIA BLATTAE
Keywords keywords	ALL ALPHA, HYDROLASE; HYDROLASE
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	18.06 Å
Radius of gyration Rg (electron density) rg_electron	17.38 Å
Forward intensity I(0) i0	11067400.00
Molecular weight molecular_weight	24157.0 kDa
Excluded volume excluded_volume	29926 Å³
Envelope volume envelope_volume	33237 Å³
Hydration-shell volume shell_volume	16223 Å³
Envelope diameter envelope_diameter	61.9 Å
Shell Rg shell_rg	23.32 Å
Envelope Rg envelope_rg	17.69 Å
Shape Rg shape_rg	17.38 Å
Total Rg total_rg	18.28 Å
Total atoms total_atoms	1701
Residues n_residues	222
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	61.1 Å
Rg (real space) rg_real	18.00 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	1.1070e+07
I(0) uncertainty (real space) i0_real_error	1.4690e+05
Rg (reciprocal space) rg_reciprocal	18.00 Å
I(0) (reciprocal space) i0_reciprocal	11070000.0000
Solution quality estimate total_estimate	0.8032
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.5 Å
Skewness Skewness skewness	0.253
Kurtosis Kurtosis kurtosis	-0.387
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2573000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; 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	ACID PHOSPHATASE
Molecular weight formula_weight	25033.1 kDa
EC 编号 ec_number	3.1.3.2
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	1937

LALVATGNDTTTKPDLYYLKNSEAINSLALLPPPPAVGSIAFLNDQAMYEQGRLLRNTERGKLAAEDANLSSGGVANAFSGAFGSPITEKDAPALHKLLTNMIEDAGDLATRSAKDHYMRIRPFAFYGVSTCNTTEQDKLSKNGSYPSGHTSIGWATALVLAEINPQRQNEILKRGYELGQSRVICGYHWQSDVDAARVVGSAVVATLHTNPAFQQQLQKAKAEFAQHQKK

来源 Source

来源生物 organism	Escherichia blattae
NCBI Class编号 ncbi_taxonomy_id	563
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	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	236

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1d2ta_
Class class	a — All alpha proteins
Fold Fold fold	a.111 — Acid phosphatase/Vanadium-dependent haloperoxidase
Superfamily Superfamily superfamily	a.111.1 — Acid phosphatase/Vanadium-dependent haloperoxidase
Family Family family	a.111.1.1 — Type 2 phosphatidic acid phosphatase, PAP2

CATH v4.4 (1 domains)

Domain ID domain_id	1d2tA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	144 — Vanadium-containing Chloroperoxidase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphatidic acid phosphatase type 2/haloperoxidase

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8. Citations (1)

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Unit-cell length a length_a	124.700 Å
Unit-cell length b length_b	124.700 Å
Unit-cell length c length_c	97.700 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 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2150
R_work r_work	0.2160
R_free r_free	0.2570

fit	/app/data/saxs_computation/d2/1d2t/1d2t.fit
pddf	/app/data/pr_computation/d2/1d2t/1d2t.pr.out
profile	/app/data/saxs_computation/d2/1d2t/1d2t.dat

CRYSTAL STRUCTURE OF ACID PHOSPHATASE FROM ESCHERICHIA BLATTAE

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

ACID PHOSPHATASE

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