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2had

CRYSTAL STRUCTURE OF HALOALKANE DEHALOGENASE: AN ENZYME TO DETOXIFY HALOGENATED ALKANES

Method: X-RAY DIFFRACTION Dmax: 57.0 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HALOALKANE DEHALOGENASE

Xanthobacter autotrophicus

UniProt P22643

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 2HAD 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
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 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
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
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.

SAXS scattering curve SAXS Profile

SAXS profile for 2had

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2had
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2had
Deposition date deposition_date1992-08-07
Structure title titleCRYSTAL STRUCTURE OF HALOALKANE DEHALOGENASE: AN ENZYME TO DETOXIFY HALOGENATED ALKANES
Keywords keywordsDEHALOGENASE; DEHALOGENASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.50 Å
Radius of gyration Rg (electron density) rg_electron17.92 Å
Forward intensity I(0) i020514500.00
Molecular weight molecular_weight35127.0 kDa
Excluded volume excluded_volume44055 ų
Envelope volume envelope_volume48916 ų
Hydration-shell volume shell_volume21759 ų
Envelope diameter envelope_diameter58.2 Å
Shell Rg shell_rg25.31 Å
Envelope Rg envelope_rg18.21 Å
Shape Rg shape_rg17.90 Å
Total Rg total_rg18.96 Å
Total atoms total_atoms2479
Residues n_residues310
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax57.0 Å
Rg (real space) rg_real19.30 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real2.0510e+07
I(0) uncertainty (real space) i0_real_error2.3850e+05
Rg (reciprocal space) rg_reciprocal19.33 Å
I(0) (reciprocal space) i0_reciprocal20510000.0000
Solution quality estimate total_estimate0.9038
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.7 Å
Skewness Skewness skewness0.015
Kurtosis Kurtosis kurtosis-0.524
Angular range angular_range— – 0.4100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8561000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.974
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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_idd2hada_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.8 — Haloalkane dehalogenase

CATH v4.4 (1 domains)

Domain ID domain_id2hadA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
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8. Citations (2)

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9. Files and Curves (10)