SAXSdb — 1ede

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

HALOALKANE DEHALOGENASE

Xanthobacter autotrophicus

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 1–310	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å

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 1EDE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B6G HALOALKANE DEHALOGENASE AT PH 5.0 CONTAINING CHLORIDE Deposited 1999-01-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 1.15 Å R-free 0.145
1BE0 HALOALKANE DEHALOGENASE AT PH 5.0 CONTAINING ACETIC ACID Deposited 1998-05-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Mutation：I2V	ACT ACETATE ION × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；PROTEIN WAS CRYSTALLIZED FROM 50% AMMONIUM SULFATE, 100 MM MES, PH 5.6	Resolution 1.96 Å R-free 0.220
1BEE HALOALKANE DEHALOGENASE MUTANT WITH TRP 175 REPLACED BY TYR Deposited 1998-05-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Mutation：I2V, W175Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；PROTEIN WAS CRYSTALLIZED FROM 50% AMMONIUM SULFATE, 100 MM MES, PH 5.6	Resolution 2.60 Å R-free 0.253
1BEZ HALOALKANE DEHALOGENASE MUTANT WITH TRP 175 REPLACED BY TYR AT PH 5 Deposited 1998-05-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Mutation：I2V, W175Y	ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；PROTEIN WAS CRYSTALLIZED FROM 50% AMMONIUM SULFATE, 100 MM MES, PH 5.6	Resolution 2.10 Å R-free 0.225
1CIJ HALOALKANE DEHALOGENASE SOAKED WITH HIGH CONCENTRATION OF BROMIDE Deposited 1999-03-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Mutation：I2V	BR BROMIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；50 % AMMONIUM SULFATE 100 MM MES BUFFER, PH 5.9 , pH 5.8	Resolution 2.30 Å R-free 0.272
1EDB CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF HALOALKANE DEHALOGENASE WITH HALIDE IONS: STUDIES WITH HALIDE COMPOUNDS REVEAL A HALIDE BINDING SITE IN THE ACTIVE SITE Deposited 1993-05-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.01 Å
1EDD CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF HALOALKANE DEHALOGENASE WITH HALIDE IONS: STUDIES WITH HALIDE COMPOUNDS REVEAL A HALIDE BINDING SITE IN THE ACTIVE SITE Deposited 1993-05-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.19 Å
1HDE HALOALKANE DEHALOGENASE MUTANT WITH PHE 172 REPLACED WITH TRP Deposited 1996-08-08	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Mutation：F172W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；pH 5.8	Resolution 2.70 Å R-free 0.258
1HDE HALOALKANE DEHALOGENASE MUTANT WITH PHE 172 REPLACED WITH TRP Deposited 1996-08-08	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–310（310 aa）	Mutation：F172W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；pH 5.8	Resolution 2.70 Å R-free 0.258
2DHC CRYSTALLOGRAPHIC ANALYSIS OF THE CATALYTIC MECHANISM OF HALOALKANE DEHALOGENASE Deposited 1993-09-08	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Not recorded	DCE 1,2-DICHLOROETHANE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
2DHD CRYSTALLOGRAPHIC ANALYSIS OF THE CATALYTIC MECHANISM OF HALOALKANE DEHALOGENASE Deposited 1993-09-08	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.13 Å
2DHE CRYSTALLOGRAPHIC ANALYSIS OF THE CATALYTIC MECHANISM OF HALOALKANE DEHALOGENASE Deposited 1993-06-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.13 Å
2EDA CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF HALOALKANE DEHALOGENASE WITH HALIDE IONS: STUDIES WITH HALIDE COMPOUNDS REVEAL A HALIDE BINDING SITE IN THE ACTIVE SITE Deposited 1993-08-30	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Not recorded	IOD IODIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.19 Å
2EDC CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF HALOALKANE DEHALOGENASE WITH HALIDE IONS: STUDIES WITH HALIDE COMPOUNDS REVEAL A HALIDE BINDING SITE IN THE ACTIVE SITE Deposited 1993-08-31	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Not recorded	IOD IODIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
2HAD CRYSTAL STRUCTURE OF HALOALKANE DEHALOGENASE: AN ENZYME TO DETOXIFY HALOGENATED ALKANES Deposited 1992-08-07	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–310（310 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
2PKY The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase Deposited 2007-04-18	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–310（310 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2.6M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.55 Å R-free 0.231
2YXP The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase Deposited 2007-04-27	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–310（310 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；2.4M ammonium sulfate, 0.1M MES,, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.53 Å R-free 0.185

16 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DHLA_XANAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–310； UniProt 1–310

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	1ede
Deposition date deposition_date	1993-05-13
Structure title title	REFINED X-RAY STRUCTURES OF HALOALKANE DEHALOGENASE AT PH 6.2 AND PH 8.2 AND IMPLICATIONS FOR THE REACTION MECHANISM
Keywords keywords	DEHALOGENASE; DEHALOGENASE
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	19.44 Å
Radius of gyration Rg (electron density) rg_electron	17.90 Å
Forward intensity I(0) i0	20405700.00
Molecular weight molecular_weight	35127.0 kDa
Excluded volume excluded_volume	44055 Å³
Envelope volume envelope_volume	48430 Å³
Hydration-shell volume shell_volume	21627 Å³
Envelope diameter envelope_diameter	57.2 Å
Shell Rg shell_rg	25.18 Å
Envelope Rg envelope_rg	18.14 Å
Shape Rg shape_rg	17.89 Å
Total Rg total_rg	18.91 Å
Total atoms total_atoms	2479
Residues n_residues	310
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	56.4 Å
Rg (real space) rg_real	19.25 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	2.0410e+07
I(0) uncertainty (real space) i0_real_error	2.3790e+05
Rg (reciprocal space) rg_reciprocal	19.28 Å
I(0) (reciprocal space) i0_reciprocal	20410000.0000
Solution quality estimate total_estimate	0.7055
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.007
Kurtosis Kurtosis kurtosis	-0.533
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8176000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 0.132; Positv: 1.000; Valcen: 0.966; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1edea_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.8 — Haloalkane dehalogenase

CATH v4.4 (1 domains)

Domain ID domain_id	1edeA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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8. Citations (3)

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Unit-cell length a length_a	94.400 Å
Unit-cell length b length_b	72.900 Å
Unit-cell length c length_c	41.400 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1640
R_work r_work	—
R_free r_free	—

Description description	HALOALKANE DEHALOGENASE
Molecular weight formula_weight	35175.8 kDa
EC 编号 ec_number	3.8.1.5
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2683

REFINED X-RAY STRUCTURES OF HALOALKANE DEHALOGENASE AT PH 6.2 AND PH 8.2 AND IMPLICATIONS FOR THE REACTION MECHANISM

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

HALOALKANE DEHALOGENASE

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Xanthobacter autotrophicus
NCBI Class编号 ncbi_taxonomy_id	280

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

fit	/app/data/saxs_computation/ed/1ede/1ede.fit
pddf	/app/data/pr_computation/ed/1ede/1ede.pr.out
profile	/app/data/saxs_computation/ed/1ede/1ede.dat