SAXSdb — 9nfd

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

Cis-3-chloroacrylic acid dehalogenase

coryneform bacterium

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 2–150 Chain B； UniProt 2–150 Chain C； UniProt 2–150	Not recorded	FK2 3-oxidanylidenepropanoic acid × 2 A1BXY prop-2-ynoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；296 K；0.05 M citric acid, 0.05 M BIS-TRIS propane) pH 6 17% w/v PEG 3,355	Resolution 2.30 Å R-free 0.276

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 9NFD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3MF7 Crystal Structure of (R)-oxirane-2-carboxylate inhibited cis-CaaD Deposited 2010-04-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Fragment：UNP residues 2-118	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 4.6；298 K；three micro liter of 15.6mg/mL cis-CaaD protein sample mixed with three micro liter crystallization solution: 0.125 M CaCl2, 0.07 M sodium acetate buffer, 12.5% isopropanol, hanging drop, temperature 298K, pH 4.6	Resolution 1.65 Å R-free 0.222
3MF8 Crystal Structure of Native cis-CaaD Deposited 2010-04-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Fragment：UNP residues 2-118	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 9；298 K；three micro liter of 14 mg/mL cis-CaaD protein sample mixed with three micro liter crystallization solution: 8 M (NH4)2SO4, 0.1 M Bicine buffer (pH 9.0), hanging drop, temperature 298K	Resolution 2.01 Å R-free 0.236
9NF1 cis-CaaD E114D mutant Deposited 2025-02-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Mutation：E114D Mutation：E114D Mutation：E114D	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2 M ammonium sulfate 20% w/v PEG 3,351	Resolution 1.60 Å R-free 0.220
9NF3 cis-CaaD E114D mutant with a covalent ethylene intermediate of the hydration and decarboxylation of cis-3-chloroacrylic acid Deposited 2025-02-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Mutation：E114D Mutation：E114D Mutation：E114D Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2 M ammonium sulfate 20% w/v PEG 3,353	Resolution 1.80 Å R-free 0.224
9NF9 cis-CaaD E114N mutant apo Deposited 2025-02-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–150（150 aa） Chain B 1–150（150 aa） Chain C 1–150（150 aa）	Mutation：E114N Mutation：E114N Mutation：E114N	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；(0.03 M citric acid, 0.07 M BIS-TRIS propane) pH 7.6	Resolution 2.51 Å R-free 0.290
9NFF Native cis-CaaD with acetylenecarboxylic acid substrate Deposited 2025-02-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Not recorded	A1BXY prop-2-ynoic acid × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2 M ammonium tartrate dibasic, 20% w/v PEG 3,353	Resolution 2.00 Å R-free 0.262
9NFH Native cis-CaaD Deposited 2025-02-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa）	Not recorded	ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.18 M ammonium acetate 16% PEG 3,352	Resolution 1.32 Å R-free 0.213
9NG4 cis-CaaD Y103F mutant apo Deposited 2025-02-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Mutation：Y103F Mutation：Y103F Mutation：Y103F	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2 M sodium fluoride 20% w/v PEG 3,350	Resolution 2.20 Å R-free 0.274
9NG5 cis-CaaD Y103F mutant soaked with acetylencarboxylic acid Deposited 2025-02-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.2 M magnesium sulfate hep-tahydrate 20% w/v PEG 3,350	Resolution 2.28 Å R-free 0.354
9NG7 cis-CaaD H28A mutant Deposited 2025-02-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2 M ammonium acetate 20% w/v PEG 3,350	Resolution 1.80 Å R-free 0.231
9NG8 cis-CaaD T34A mutant apo Deposited 2025-02-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–150（150 aa） Chain B 1–150（150 aa） Chain C 1–150（150 aa）	Mutation：T34A Mutation：T34A Mutation：T34A	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.2 M ammonium sulfate 20% w/v PEG 3,350	Resolution 2.51 Å R-free 0.283
9NG9 cis-CaaD T34A mutant soaked with acetylenecarboxylic acid Deposited 2025-02-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–150（150 aa） Chain B 1–150（150 aa） Chain C 1–150（150 aa）	Mutation：T34A Mutation：T34A Mutation：T34A	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.2 M ammonium sulfate 20% w/v PEG 3,350	Resolution 2.35 Å R-free 0.280
9NGA cis-CaaD T34A mutant soaked with cis-3-chloroacrylic acid Deposited 2025-02-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Mutation：T34A Mutation：T34A Mutation：T34A	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.2 M ammonium sulfate 20% w/v PEG 3,350	Resolution 2.40 Å R-free 0.308
9NGB truncated cis-CaaD Deposited 2025-02-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–120（119 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2 M ammonium sulfate 20% w/v PEG 3,350	Resolution 2.50 Å R-free 0.301
9NGD cis-CaaD/Cg10062 chimera Deposited 2025-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–120（119 aa）	Not recorded	CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2 M lithium chloride 20% w/v PEG 3,350	Resolution 2.70 Å R-free 0.336
9NGL cis-CaaD E114Q Deposited 2025-02-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Mutation：E114Q Mutation：E114Q Mutation：E114Q	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；(0.05 M citric acid, 0.05 M BIS-TRIS propane) pH 5 20% w/v PEG 3,354	Resolution 1.80 Å R-free 0.215
9O2N cis-CaaD Y103F mutant soaked with cis-3-chloroacrylic acid Deposited 2025-04-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2 M sodium fluoride 20% w/v PEG 3,350	Resolution 2.20 Å R-free 0.237
9YRI cis-CaaD E114Q mutant with covalent intermediates of the hydration and decarboxylation of acetylenecarboxylic acid Deposited 2025-10-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Mutation：E114Q Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E114Q Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E114Q Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；(0.05 citric acid, 0.05 BIS-TRIS propane) pH 5 20% w/v PEG 3,352	Resolution 2.20 Å R-free 0.241
9YRJ Cis-CaaD E114Q mutant with a covalent hydroxypropionate intermediate of the hydration of acetylenecarboxylic acid Deposited 2025-10-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Mutation：E114Q Mutation：E114Q Mutation：E114Q	3OH 3-HYDROXY-PROPANOIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；(0.05 M citric acid, 0.05 M BIS-TRIS propane) pH 5 20% w/v PEG 3,350	Resolution 1.93 Å R-free 0.240
9YTU cis-CaaD E114D mutant with a covalent intermediates of the hydration of acetylenecarboxylic acid Deposited 2025-10-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Chain B 2–150（149 aa） Chain C 2–150（149 aa）	Mutation：E114D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E114D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E114D	A1BXY prop-2-ynoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.2 M ammonium sulfate 20% w/v PEG 3,360	Resolution 2.51 Å R-free 0.260

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6VPE5_9CORY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 2–150 Author chain B； PDBConstruct 1–149； UniProt 2–150 Author chain C； PDBConstruct 1–149； UniProt 2–150

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	9nfd
Deposition date deposition_date	2025-02-21
最后修订 last_revision	2025-04-02
Structure title title	cis-CaaD E114N mutant with acetylenecarboxylic acid substrate and hydration product malonic semialdehyde
Keywords keywords	Tautomerase, cis-CaaD, acetylenecarboxylic acid, 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	21.66 Å
Radius of gyration Rg (electron density) rg_electron	20.62 Å
Forward intensity I(0) i0	76771200.00
Molecular weight molecular_weight	45384.0 kDa
Excluded volume excluded_volume	43442 Å³
Envelope volume envelope_volume	67524 Å³
Hydration-shell volume shell_volume	26311 Å³
Envelope diameter envelope_diameter	65.0 Å
Shell Rg shell_rg	28.32 Å
Envelope Rg envelope_rg	20.78 Å
Shape Rg shape_rg	20.59 Å
Total Rg total_rg	21.29 Å
Total atoms total_atoms	3440
Residues n_residues	435
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	64.5 Å
Rg (real space) rg_real	21.49 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	7.6770e+07
I(0) uncertainty (real space) i0_real_error	9.4710e+05
Rg (reciprocal space) rg_reciprocal	21.52 Å
I(0) (reciprocal space) i0_reciprocal	76770000.0000
Solution quality estimate total_estimate	0.9087
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.127
Kurtosis Kurtosis kurtosis	-0.480
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19970000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.943; 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 (4)

Entity 1 Entity 1 polymer

Description description	Cis-3-chloroacrylic acid dehalogenase
Molecular weight formula_weight	18552.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,A
Atom count atom_count	3594

PVYMVYVSQDRLTPSAKHAVAKAITDAHRGLTGTQHFLAQVNFQEQPAGNVFLGGVQQGGDTIFVHGLHREGRSADLKGQLAQRIVDDVSVAAEIDRKHIWVYFGEMPAQQMVNYGRFLPQPGHEGEWFDNLSSDERAFMETNVDVSRTENLYFQGLEHHHHHH

来源 Source

来源生物 organism	coryneform bacterium
NCBI Class编号 ncbi_taxonomy_id	1728
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	3-oxidanylidenepropanoic acid
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	prop-2-ynoic acid
Molecular weight formula_weight	70.0 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	154

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8. Citations (1)

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Unit-cell length a length_a	60.405 Å
Unit-cell length b length_b	100.972 Å
Unit-cell length c length_c	148.185 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	orthorhombic

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	35.310 Å
R factor r_factor	0.2112
R_work r_work	0.2038
R_free r_free	0.2758

fit	/app/data/saxs_computation/nf/9nfd/9nfd.fit
pddf	/app/data/pr_computation/nf/9nfd/9nfd.pr.out
profile	/app/data/saxs_computation/nf/9nfd/9nfd.dat

cis-CaaD E114N mutant with acetylenecarboxylic acid substrate and hydration product malonic semialdehyde

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

Cis-3-chloroacrylic acid 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