SAXSdb — 1edd

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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	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.19 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 1EDD	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 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	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 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
1EDE REFINED X-RAY STRUCTURES OF HALOALKANE DEHALOGENASE AT PH 6.2 AND PH 8.2 AND IMPLICATIONS FOR THE REACTION MECHANISM 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	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1HDE HALOALKANE DEHALOGENASE MUTANT WITH PHE 172 REPLACED WITH TRP Deposited 1996-08-08	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：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 ligand/ion 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 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 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	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	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	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 ligand/ion 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 ligand/ion 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	1edd
Deposition date deposition_date	1993-05-13
Structure title title	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
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	19.42 Å
Radius of gyration Rg (electron density) rg_electron	17.85 Å
Forward intensity I(0) i0	20652800.00
Molecular weight molecular_weight	35162.0 kDa
Excluded volume excluded_volume	44078 Å³
Envelope volume envelope_volume	48322 Å³
Hydration-shell volume shell_volume	21597 Å³
Envelope diameter envelope_diameter	57.3 Å
Shell Rg shell_rg	25.23 Å
Envelope Rg envelope_rg	18.13 Å
Shape Rg shape_rg	17.84 Å
Total Rg total_rg	18.89 Å
Total atoms total_atoms	2480
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	56.8 Å
Rg (real space) rg_real	19.22 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	2.0650e+07
I(0) uncertainty (real space) i0_real_error	2.2400e+05
Rg (reciprocal space) rg_reciprocal	19.25 Å
I(0) (reciprocal space) i0_reciprocal	20650000.0000
Solution quality estimate total_estimate	0.9052
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.015
Kurtosis Kurtosis kurtosis	-0.526
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8754000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.992

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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	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 Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2652

MINAIRTPDQRFSNLDQYPFSPNYLDDLPGYPGLRAHYLDEGNSDAEDVFLCLHGEPTWSYLYRKMIPVFAESGARVIAPDFFGFGKSDKPVDEEDYTFEFHRNFLLALIERLDLRNITLVVQDWGGFLGLTLPMADPSRFKRLIIMNACLMTDPVTQPAFSAFVTQPADGFTAWKYDLVTPSDLRLDQFMKRWAPTLTEAEASAYAAPFPDTSYQAGVRKFPKMVAQRDQACIDISTEAISFWQNDWNGQTFMAIGMKDKLLGPDVMYPMKALINGCPEPLEIADAGHFVQEFGEQVAREALKHFAETE

来源 Source

来源生物 organism	Xanthobacter autotrophicus
NCBI Class编号 ncbi_taxonomy_id	280

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	172

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1edda_
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	1eddA00
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	72.500 Å
Unit-cell length c length_c	41.300 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	2.190 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1810
R_work r_work	—
R_free r_free	—

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

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

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