SAXSdb — 1k6e

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

HALOALKANE DEHALOGENASE

Sphingomonas paucimobilis

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 2–296	Not recorded	BR BROMIDE ION × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 3 PGO S-1,2-PROPANEDIOL × 1 1BP 1-BROMOPROPANE-2-OL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.2；289 K；PEG 4000,magnesium chloride, TRIS, pH 8.20, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K	Resolution 1.85 Å R-free 0.201

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 1K6E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CV2 Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 AT 1.6 A resolution Deposited 1999-08-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–296（296 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；278 K；19% (W/V) PEG 6000, 100 MM TRIS-HCL, 200MM CA ACETATE, PH=8.9, VAPOR DIFFUSION, HANGING DROP at 278K	Resolution 1.58 Å R-free 0.211
1D07 Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A resolution Deposited 1999-09-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–296（296 aa）	Not recorded	BR BROMIDE ION × 2 PDO 1,3-PROPANDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；278 K；19% (W/V) PEG 6000, 100 MM TRIS-HCL, 200MM CA ACETATE, PH=8.9 VAPOR DIFFUSION, HANGING DROP. CRYSTAL WAS SOAKED 4 HOURS IN RESERVOIR LIQUOR WITH 25MM 1,3-DIBROMPROPANE AT 278K	Resolution 2.00 Å R-free 0.274
1G42 STRUCTURE OF 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE (LINB) FROM SPHINGOMONAS PAUCIMOBILIS COMPLEXED WITH 1,2-DICHLOROPROPANE Deposited 2000-10-26	Different construct 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 1–296（296 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 1 CA CALCIUM ION × 3 CL CHLORIDE ION × 1 CP2 1,2-DICHLORO-PROPANE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；278 K；0.1 M Tris-HCl pH 8.9, 18-20%(w/v) PEG 6000, 0.2 M calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 1.80 Å R-free 0.193
1G4H LINB COMPLEXED WITH BUTAN-1-OL Deposited 2000-10-27	Different construct 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 1–296（296 aa）	Mutation：R291(2MR) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 CL CHLORIDE ION × 1 1BO 1-BUTANOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；298 K；18-20% PEG 6000, 0.2 M Calcium Acetate, 0.1 M Tris-HCl pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.201
1G5F STRUCTURE OF LINB COMPLEXED WITH 1,2-DICHLOROETHANE Deposited 2000-11-01	Different construct 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 1–296（296 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 3 CL CHLORIDE ION × 1 DCE 1,2-DICHLOROETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；278 K；0.2 M Calcium Acetate, 18-20% PEG 6000, 0.1 M Tris Buffer pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 1.80 Å R-free 0.198
1IZ7 Re-refinement of the structure of hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 AT 1.6 A resolution Deposited 2002-09-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–296（295 aa）	Not recorded	CL CHLORIDE ION × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.58 Å R-free 0.178
1IZ8 Re-refinement of the structure of hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A resolution Deposited 2002-09-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–296（295 aa）	Not recorded	BR BROMIDE ION × 1 CA CALCIUM ION × 3 PDO 1,3-PROPANDIOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.248
1K5P Hydrolytic haloalkane dehalogenase LINB from sphingomonas paucimobilis UT26 at 1.8A resolution Deposited 2001-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–296（295 aa）	Not recorded	CL CHLORIDE ION × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；PEG 4000, TRIS, magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.226
1K63 Complex of hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis with UT26 2-BROMO-2-PROPENE-1-OL at 1.8A resolution Deposited 2001-10-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–296（295 aa）	Not recorded	BR BROMIDE ION × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 3 BRP 2-BROMO-2-PROPENE-1-OL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；PEG 4000, magnesium chloride, TRIS , pH 8.20, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.200
1MJ5 LINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT26 at atomic resolution Deposited 2002-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–296（296 aa）	Not recorded	MG MAGNESIUM ION × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；200 mM MgCl2, 100 mM Tris HCl pH 8.5, 20% (w/v) PEG 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 0.95 Å R-free 0.141
2BFN The crystal structure of the complex of the haloalkane dehalogenase LinB with the product of dehalogenation reaction 1,2-dichloropropane. Deposited 2004-12-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–296（296 aa）	Not recorded	D2P (2S)-2,3-DICHLOROPROPAN-1-OL × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å R-free 0.171
4WDQ Crystal structure of haloalkane dehalogenase LinB32 mutant (L177W) from Sphingobium japonicum UT26 Deposited 2014-09-09	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 2–296（295 aa）	Mutation：L177W	MG MAGNESIUM ION × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；0.1M MES; 0.2M MgCl2; 25% PEG3350	Resolution 1.58 Å R-free 0.206

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LINB_PSEPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–295； UniProt 2–296

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	1k6e
Deposition date deposition_date	2001-10-16
Structure title title	COMPLEX OF HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,2-PROPANEDIOL (PRODUCT OF DEHALOGENATION OF 1,2-DIBROMOPROPANE) AT 1.85A
Keywords keywords	DEHALOGENASE, LINDANE, BIODEGRADATION, ALPHA/BETA-HYDROLASE, 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	18.80 Å
Radius of gyration Rg (electron density) rg_electron	17.46 Å
Forward intensity I(0) i0	19381800.00
Molecular weight molecular_weight	33259.0 kDa
Excluded volume excluded_volume	41358 Å³
Envelope volume envelope_volume	44628 Å³
Hydration-shell volume shell_volume	20546 Å³
Envelope diameter envelope_diameter	61.0 Å
Shell Rg shell_rg	24.61 Å
Envelope Rg envelope_rg	17.68 Å
Shape Rg shape_rg	17.44 Å
Total Rg total_rg	18.43 Å
Total atoms total_atoms	2337
Residues n_residues	295
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	60.5 Å
Rg (real space) rg_real	18.63 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	1.9380e+07
I(0) uncertainty (real space) i0_real_error	2.2860e+05
Rg (reciprocal space) rg_reciprocal	18.66 Å
I(0) (reciprocal space) i0_reciprocal	19380000.0000
Solution quality estimate total_estimate	0.8762
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	58.9 Å
Skewness Skewness skewness	0.039
Kurtosis Kurtosis kurtosis	-0.468
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8787000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	HALOALKANE DEHALOGENASE
Molecular weight formula_weight	33013.4 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	2817

SLGAKPFGEKKFIEIKGRRMAYIDEGTGDPILFQHGNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHRDYLDALWEALDLGDRVVLVVHDWGSALGFDWARRHRERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPLSEAEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPKLFINAEPGALTTGRMRDFCRTWPNQTEITVAGAHFIQEDSPDEIGAAIAAFVRRLRPA

来源 Source

来源生物 organism	Sphingomonas paucimobilis
NCBI Class编号 ncbi_taxonomy_id	13689
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	S-1,2-PROPANEDIOL
Molecular weight formula_weight	76.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1-BROMOPROPANE-2-OL
Molecular weight formula_weight	139.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	468

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1k6ea_
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	1k6eA00
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 (1)

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Unit-cell length a length_a	46.410 Å
Unit-cell length b length_b	68.330 Å
Unit-cell length c length_c	80.980 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	34.690 Å
R factor r_factor	0.1420
R_work r_work	0.1420
R_free r_free	0.2010

fit	/app/data/saxs_computation/k6/1k6e/1k6e.fit
pddf	/app/data/pr_computation/k6/1k6e/1k6e.pr.out
profile	/app/data/saxs_computation/k6/1k6e/1k6e.dat

COMPLEX OF HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,2-PROPANEDIOL (PRODUCT OF DEHALOGENATION OF 1,2-DIBROMOPROPANE) AT 1.85A