SAXSdb — 1d07

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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 1–296	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

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 1D07	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 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
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 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 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 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 construct 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 construct 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 construct 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 construct 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
1K6E COMPLEX OF HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,2-PROPANEDIOL (PRODUCT OF DEHALOGENATION OF 1,2-DIBROMOPROPANE) AT 1.85A Deposited 2001-10-16	Different construct 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 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
1MJ5 LINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT26 at atomic resolution Deposited 2002-08-27	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 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 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 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 1–296； UniProt 1–296

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	1d07
Deposition date deposition_date	1999-09-09
Structure title title	Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A resolution
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	18.65 Å
Radius of gyration Rg (electron density) rg_electron	17.36 Å
Forward intensity I(0) i0	18770300.00
Molecular weight molecular_weight	32809.0 kDa
Excluded volume excluded_volume	40857 Å³
Envelope volume envelope_volume	43597 Å³
Hydration-shell volume shell_volume	20254 Å³
Envelope diameter envelope_diameter	61.0 Å
Shell Rg shell_rg	24.45 Å
Envelope Rg envelope_rg	17.54 Å
Shape Rg shape_rg	17.35 Å
Total Rg total_rg	18.30 Å
Total atoms total_atoms	2308
Residues n_residues	293
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	59.4 Å
Rg (real space) rg_real	18.48 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	1.8770e+07
I(0) uncertainty (real space) i0_real_error	2.1710e+05
Rg (reciprocal space) rg_reciprocal	18.51 Å
I(0) (reciprocal space) i0_reciprocal	18770000.0000
Solution quality estimate total_estimate	0.8802
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.032
Kurtosis Kurtosis kurtosis	-0.477
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8191000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	HALOALKANE DEHALOGENASE
Molecular weight formula_weight	33144.6 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	2577

MSLGAKPFGEKKFIEIKGRRMAYIDEGTGDPILFQHGNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHRDYLDALWEALDLGDRVVLVVHDWGSALGFDWARRHRERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPLSEAEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPKLFINAEPGALTTGRMRDFCRTWPNQTEITVAGAHFIQEDSPDEIGAAIAAFVRRLRPA

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	1,3-PROPANDIOL
Molecular weight formula_weight	76.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	269

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1d07a_
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	1d07A00
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 (2)

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Unit-cell length a length_a	50.227 Å
Unit-cell length b length_b	71.721 Å
Unit-cell length c length_c	73.319 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	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1693
R_work r_work	—
R_free r_free	0.2737

fit	/app/data/saxs_computation/d0/1d07/1d07.fit
pddf	/app/data/pr_computation/d0/1d07/1d07.pr.out
profile	/app/data/saxs_computation/d0/1d07/1d07.dat

Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A resolution

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

Diffraction experiment Diffraction