SAXSdb — 9wtk

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

Mono-ethylhexylphthalate hydrolase

Rhodococcus sp. EG-5

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 1–303	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 6 EDO 1,2-ETHANEDIOL × 4 PHT PHTHALIC ACID × 1 1BO 1-BUTANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 6.0	Resolution 2.80 Å R-free 0.286
10	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain J； UniProt 1–303	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 5 EDO 1,2-ETHANEDIOL × 5 PHT PHTHALIC ACID × 1 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 6.0	Resolution 2.80 Å R-free 0.286
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–303	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 13 PHT PHTHALIC ACID × 1 1BO 1-BUTANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 6.0	Resolution 2.80 Å R-free 0.286
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–303	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 3 EDO 1,2-ETHANEDIOL × 5 PHT PHTHALIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 6.0	Resolution 2.80 Å R-free 0.286
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–303	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 7 EDO 1,2-ETHANEDIOL × 6 PHT PHTHALIC ACID × 1 1BO 1-BUTANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 6.0	Resolution 2.80 Å R-free 0.286
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 1–303	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 7 EDO 1,2-ETHANEDIOL × 4 PHT PHTHALIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 6.0	Resolution 2.80 Å R-free 0.286
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 1–303	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 5 EDO 1,2-ETHANEDIOL × 7 PHT PHTHALIC ACID × 1 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 6.0	Resolution 2.80 Å R-free 0.286
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 1–303	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 4 EDO 1,2-ETHANEDIOL × 8 PHT PHTHALIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 6.0	Resolution 2.80 Å R-free 0.286
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 1–303	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 5 PHT PHTHALIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 6.0	Resolution 2.80 Å R-free 0.286
9	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain I； UniProt 1–303	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 4 EDO 1,2-ETHANEDIOL × 4 PHT PHTHALIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 6.0	Resolution 2.80 Å R-free 0.286

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 9WTK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
26QV Crystal structure of monoalkyl phthalate hydrolase from Rhodococcus sp. EG-5 Deposited 2026-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–303（303 aa） Chain B 1–303（303 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.294
26QV Crystal structure of monoalkyl phthalate hydrolase from Rhodococcus sp. EG-5 Deposited 2026-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–303（303 aa） Chain D 1–303（303 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.294
26QV Crystal structure of monoalkyl phthalate hydrolase from Rhodococcus sp. EG-5 Deposited 2026-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–303（303 aa） Chain H 1–303（303 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.294
26QV Crystal structure of monoalkyl phthalate hydrolase from Rhodococcus sp. EG-5 Deposited 2026-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain F 1–303（303 aa） Chain G 1–303（303 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.294
26QV Crystal structure of monoalkyl phthalate hydrolase from Rhodococcus sp. EG-5 Deposited 2026-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 1–303（303 aa） Chain J 1–303（303 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.294

1 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0U5ADH4_9NOCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–303； UniProt 1–303 Author chain B； PDBConstruct 1–303； UniProt 1–303 Author chain C； PDBConstruct 1–303； UniProt 1–303 Author chain D； PDBConstruct 1–303； UniProt 1–303 Author chain E； PDBConstruct 1–303； UniProt 1–303 Author chain F； PDBConstruct 1–303； UniProt 1–303 Author chain G； PDBConstruct 1–303； UniProt 1–303 Author chain H； PDBConstruct 1–303； UniProt 1–303 Author chain I； PDBConstruct 1–303； UniProt 1–303 Author chain J； PDBConstruct 1–303； UniProt 1–303

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	9wtk
Deposition date deposition_date	2025-09-16
最后修订 last_revision	2026-05-27
Structure title title	Crystal structure of monoalkyl phthalate hydrolase in complex with MBP from Rhodococcus sp. EG-5
Keywords keywords	Mono-butyl phthalate, 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	69.00 Å
Radius of gyration Rg (electron density) rg_electron	69.65 Å
Forward intensity I(0) i0	1442650000.00
Molecular weight molecular_weight	325130.0 kDa
Excluded volume excluded_volume	409150 Å³
Envelope volume envelope_volume	608010 Å³
Hydration-shell volume shell_volume	79478 Å³
Envelope diameter envelope_diameter	251.3 Å
Shell Rg shell_rg	60.67 Å
Envelope Rg envelope_rg	68.16 Å
Shape Rg shape_rg	69.65 Å
Total Rg total_rg	69.45 Å
Total atoms total_atoms	22922
Residues n_residues	2905
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	225.9 Å
Rg (real space) rg_real	69.50 Å
Rg uncertainty (real space) rg_real_error	2.55 Å
I(0) (real space) i0_real	1.4420e+09
I(0) uncertainty (real space) i0_real_error	3.6770e+07
Rg (reciprocal space) rg_reciprocal	66.84 Å
I(0) (reciprocal space) i0_reciprocal	1435000000.0000
Solution quality estimate total_estimate	0.7981
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	49.1 Å
Skewness Skewness skewness	0.572
Kurtosis Kurtosis kurtosis	-0.328
Angular range angular_range	— – 0.1150 Å⁻¹
Current regularization parameter α current_alpha	0.0009
Highest regularization parameter α highest_alpha	39050000.0000
Real-space data points n_real_points	24
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.732; Smooth: 0.188

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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	Mono-ethylhexylphthalate hydrolase
Molecular weight formula_weight	33066.5 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	22926

MNTDLSVNYISVGGIRTRYIDQGEGPVILLIHGGHSGMSMPVGGDGWAPVIAPLVDKGFRVVTFDKLGQGETDLAPTHAEWTFDAVVKHARGFIDALGLEDMILVGHSRGGLLASKLALDMPESTKGLFIVSSATLAGTDAKFRDVEFYDAITRSLPADASPEEICGAYFRALYVTPVPQEQINAAAAKYVKENHQNALKTYPMVEKKYWEPSLQAAKDDIRARLFAGEVNIPVEVVWGRDDRSAPVDLGIAFYQKLALVSETTSLHILGTAGHNVFAERTEDFVRILADYAGRRSASYATRR

来源 Source

来源生物 organism	Rhodococcus sp. EG-5
NCBI Class编号 ncbi_taxonomy_id	1747801
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	44

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	61

Entity 4 Entity 4 non-polymer

Description description	PHTHALIC ACID
Molecular weight formula_weight	166.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

Description description	1-BUTANOL
Molecular weight formula_weight	74.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 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	4

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8. Citations (1)

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Unit-cell length a length_a	176.313 Å
Unit-cell length b length_b	244.890 Å
Unit-cell length c length_c	192.097 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	80

Space group space_group	C 2 2 2
Space-group number int_tables_number	21
Crystal system crystal_system	orthorhombic

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	24.290 Å
R factor r_factor	0.2584
R_work r_work	0.2569
R_free r_free	0.2864

fit	/app/data/saxs_computation/wt/9wtk/9wtk.fit
pddf	/app/data/pr_computation/wt/9wtk/9wtk.pr.out
profile	/app/data/saxs_computation/wt/9wtk/9wtk.dat

Crystal structure of monoalkyl phthalate hydrolase in complex with MBP from Rhodococcus sp. EG-5

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

Mono-ethylhexylphthalate hydrolase

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