PDB-4dnq: Crystal Structure of DAD2 S96A mutant

ID or keywords:

Entry

Database: PDB / ID: 4dnq

Title

Crystal Structure of DAD2 S96A mutant

Components

DAD2

Keywords

HYDROLASE / alpha/beta hydrolase

Function / homology

Function and homology information

strigolactone biosynthetic process / secondary shoot formation / hydrolase activity, acting on ester bonds / Hydrolases; Acting on ester bonds
Similarity search - Function

Biological species

Petunia hybrida (garden petunia)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.8 Å

Authors

Hamiaux, C.

Citation

Journal: Curr.Biol. / Year: 2012
Title: DAD2 Is an alpha/beta Hydrolase likely to Be Involved in the Perception of the Plant Branching Hormone, Strigolactone
Authors: Hamiaux, C. / Drummond, R.S. / Janssen, B.J. / Ledger, S.E. / Cooney, J.M. / Newcomb, R.D. / Snowden, K.C.

History

Deposition	Feb 8, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 14, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 26, 2013	Group: Database references
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4dnq.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4dnq.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	4dnq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4dnq_validation.pdf.gz	515.2 KB	Display	wwPDB validaton report
Full document	4dnq_full_validation.pdf.gz	590.8 KB	Display
Data in XML	4dnq_validation.xml.gz	112 KB	Display
Data in CIF	4dnq_validation.cif.gz	149.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dn/4dnq ftp://data.pdbj.org/pub/pdb/validation_reports/dn/4dnq	HTTPS FTP

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Related structure data

Related structure data	4dnpC C: citing same article (ref.)
Similar structure data	3w05-2 6elx-1 4ih4-3 6ap6-2 5h0k-d 5zhs-d 4ih9-2 5yz7-2 3vxk-2 3gvz-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4dnpC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: DAD2

B: DAD2

C: DAD2

D: DAD2

E: DAD2

F: DAD2

G: DAD2

H: DAD2

I: DAD2

J: DAD2

K: DAD2

L: DAD2

358 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

9

I: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

10

J: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

11

K: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

12

L: DAD2

defined by author&software
29.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	176.660, 176.660, 107.670
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	4 - 266
2	1	1	2	B	4 - 266
3	1	1	2	C	4 - 266
4	1	1	2	D	4 - 266
5	1	1	2	E	4 - 266
6	1	1	2	F	4 - 266
7	1	1	2	G	4 - 266
8	1	1	2	H	4 - 266
9	1	1	2	I	4 - 266
10	1	1	2	J	4 - 266
11	1	1	2	K	4 - 266
12	1	1	2	L	4 - 266

#1: Protein	DAD2 Mass: 29845.180 Da / Num. of mol.: 12 / Mutation: S96A Source method: isolated from a genetically manipulated source Details: gene was codon optimized for E.coli expression / Source: (gene. exp.) Petunia hybrida (garden petunia) / Gene: dad2 / Plasmid: pDEST566 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami 2 / References: UniProt: J9U5U9*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.59 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 6.6 Details: (NH4)2HPO4 0.2M, PEG 3350 18%, pH 6.6, vapor diffusion, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX2 / Wavelength: 0.978916 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.978916 Å / Relative weight: 1

Reflection

Resolution: 2.8→62.36 Å / Num. all: 92560 / Num. obs: 92560 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / B_iso Wilson estimate: 56.6 Å² / R_merge(I) obs: 0.182 / R_sym value: 0.182 / Net I/σ(I): 10.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.8-2.95	10.9	0.53	4.5	147278	13513	0.53	100
2.95-3.13	11	0.346	6.5	140670	12806	0.346	100
3.13-3.35	11.1	0.269	8.1	134126	12059	0.269	100
3.35-3.61	11.3	0.202	10.3	126342	11178	0.202	100
3.61-3.96	11.4	0.166	12.2	116903	10278	0.166	100
3.96-4.43	11.3	0.151	13.7	105230	9302	0.151	100
4.43-5.11	11.3	0.156	14.3	92225	8197	0.156	100
5.11-6.26	11	0.164	13.8	76261	6955	0.164	100
6.26-8.85	10.8	0.145	14.5	57489	5342	0.145	100
8.85-62.36	11.5	0.145	15.9	33650	2930	0.145	99.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 38.77 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.8 Å	62.36 Å
Translation	2.8 Å	62.36 Å

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.16	data scaling
PHASER	2.1.4	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
Blu-Ice		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→62.36 Å / Cor.coef. F_o:F_c: 0.891 / Cor.coef. F_o:F_c free: 0.858 / WR_factor R_free: 0.2874 / WR_factor R_work: 0.2559 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8206 / SU B: 34.758 / SU ML: 0.322 / SU R Cruickshank DPI: 0.3836 / SU R_free: 0.4128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2715	4632	5 %	RANDOM
R_work	0.2423	87904	-	-
obs	0.2437	92536	99.99 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 186.89 Å² / B_iso mean: 52.6304 Å² / B_iso min: 12.31 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.4 Å²	-0.2 Å²	0 Å²
2-	-	-0.4 Å²	0 Å²
3-	-	-	0.6 Å²

Refine analyze

Luzzati coordinate error free: 0.437 Å

Refinement step

Cycle: LAST / Resolution: 2.8→62.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24719	0	0	323	25042

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	25337
X-RAY DIFFRACTION	r_angle_refined_deg	1.463	1.95	34486
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.795	5	3141
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.878	22.595	1183
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.336	15	3926
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.14	15	216
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	3895
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	19504
X-RAY DIFFRACTION	r_mcbond_it	0.329	1.5	15667
X-RAY DIFFRACTION	r_mcangle_it	0.611	2	25218
X-RAY DIFFRACTION	r_scbond_it	1.023	3	9670
X-RAY DIFFRACTION	r_scangle_it	1.509	4.5	9268

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1048	TIGHT POSITIONAL	0.06	0.05
2	B	1048	TIGHT POSITIONAL	0.06	0.05
3	C	1048	TIGHT POSITIONAL	0.06	0.05
4	D	1048	TIGHT POSITIONAL	0.06	0.05
5	E	1048	TIGHT POSITIONAL	0.06	0.05
6	F	1048	TIGHT POSITIONAL	0.06	0.05
7	G	1048	TIGHT POSITIONAL	0.06	0.05
8	H	1048	TIGHT POSITIONAL	0.06	0.05
9	I	1048	TIGHT POSITIONAL	0.06	0.05
10	J	1048	TIGHT POSITIONAL	0.05	0.05
11	K	1048	TIGHT POSITIONAL	0.05	0.05
12	L	1048	TIGHT POSITIONAL	0.05	0.05
1	A	1006	MEDIUM POSITIONAL	0.07	0.5
2	B	1006	MEDIUM POSITIONAL	0.07	0.5
3	C	1006	MEDIUM POSITIONAL	0.07	0.5
4	D	1006	MEDIUM POSITIONAL	0.06	0.5
5	E	1006	MEDIUM POSITIONAL	0.07	0.5
6	F	1006	MEDIUM POSITIONAL	0.07	0.5
7	G	1006	MEDIUM POSITIONAL	0.07	0.5
8	H	1006	MEDIUM POSITIONAL	0.07	0.5
9	I	1006	MEDIUM POSITIONAL	0.06	0.5
10	J	1006	MEDIUM POSITIONAL	0.06	0.5
11	K	1006	MEDIUM POSITIONAL	0.07	0.5
12	L	1006	MEDIUM POSITIONAL	0.06	0.5
1	A	1048	TIGHT THERMAL	0.13	0.5
2	B	1048	TIGHT THERMAL	0.11	0.5
3	C	1048	TIGHT THERMAL	0.12	0.5
4	D	1048	TIGHT THERMAL	0.11	0.5
5	E	1048	TIGHT THERMAL	0.11	0.5
6	F	1048	TIGHT THERMAL	0.12	0.5
7	G	1048	TIGHT THERMAL	0.11	0.5
8	H	1048	TIGHT THERMAL	0.11	0.5
9	I	1048	TIGHT THERMAL	0.11	0.5
10	J	1048	TIGHT THERMAL	0.09	0.5
11	K	1048	TIGHT THERMAL	0.1	0.5
12	L	1048	TIGHT THERMAL	0.1	0.5
1	A	1006	MEDIUM THERMAL	0.13	2
2	B	1006	MEDIUM THERMAL	0.13	2
3	C	1006	MEDIUM THERMAL	0.13	2
4	D	1006	MEDIUM THERMAL	0.13	2
5	E	1006	MEDIUM THERMAL	0.13	2
6	F	1006	MEDIUM THERMAL	0.12	2
7	G	1006	MEDIUM THERMAL	0.12	2
8	H	1006	MEDIUM THERMAL	0.12	2
9	I	1006	MEDIUM THERMAL	0.12	2
10	J	1006	MEDIUM THERMAL	0.11	2
11	K	1006	MEDIUM THERMAL	0.11	2
12	L	1006	MEDIUM THERMAL	0.11	2

LS refinement shell

Resolution: 2.8→2.873 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.314	314	-
R_work	0.264	6554	-
all	-	6868	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.0128	0.7888	-0.6536	5.1863	0.2351	3.5979	-0.0246	-0.1664	0.292	0.3607	0.0552	0.1843	-0.1198	0.0716	-0.0306	0.0598	0.0212	-0.0447	0.0304	-0.0419	0.1265	79.1965	-19.3161	15.3724
2	4.8425	0.5659	0.3989	3.1995	0.1396	2.8654	-0.0456	-0.3078	-0.297	0.425	0.0831	-0.1156	-0.0591	-0.2348	-0.0375	0.1427	-0.0373	0.1034	0.2075	-0.1014	0.1821	65.758	26.5285	17.2871
3	3.4696	-0.4831	-0.4674	3.642	-0.5999	1.9401	-0.0351	-0.0814	-0.1188	-0.1393	-0.0307	-0.7288	0.3003	0.4966	0.0658	0.0908	0.0872	0.0271	0.3281	-0.0433	0.1717	32.3243	-9.1012	17.809
4	3.9852	1.1801	1.6837	3.455	0.598	3.3658	-0.1372	0.279	0.4726	-0.1264	-0.0881	0.2256	-0.305	-0.1405	0.2253	0.0994	-0.009	-0.033	0.2456	0.0382	0.061	-3.0812	3.4639	-0.5536
5	3.2609	0.4906	1.003	3.1922	-0.9542	3.4213	-0.122	0.5224	-0.2778	-0.5914	0.3971	0.2519	0.3672	-0.1537	-0.2751	0.1898	-0.1258	-0.0104	0.3759	-0.0643	0.0918	33.3978	20.3207	-2.4579
6	3.1719	-1.6603	-0.5718	4.8901	-0.7388	1.3107	0.1297	0.2351	0.2786	-0.2697	-0.2033	-0.3051	0.0902	0.017	0.0736	0.1039	-0.0015	0.0412	0.1712	0.0149	0.2241	93.0169	11.5885	-2.1349
7	2.0039	-0.1139	-0.0803	3.8303	-0.8461	4.9499	0.0498	-0.0467	-0.031	0.6171	-0.0548	0.0517	-0.0518	-0.2178	0.0051	0.2439	0.0156	-0.0423	0.1881	0.0632	0.0521	24.5926	-43.2475	25.4851
8	2.296	-0.1503	-0.3716	3.9295	0.4422	5.0154	-0.0067	-0.0869	0.1865	-0.0424	0.0741	-0.2338	-0.5277	0.204	-0.0673	0.1534	0.0405	0.0331	0.1921	-0.0979	0.1141	38.9777	50.1882	26.225
9	7.1278	-2.6472	-1.4035	3.6139	0.6849	2.9268	-0.3499	0.778	-1.6056	0.0765	-0.1938	0.7865	0.5224	0.0522	0.5437	0.1265	-0.0001	0.1518	0.1473	-0.2158	0.5648	84.4456	-56.2001	-3.91
10	1.9978	-0.8863	0.4629	8.2753	-0.4011	4.2769	0.2166	0.1959	0.265	-0.2875	-0.5131	-1.8956	-0.8608	0.3117	0.2965	0.265	-0.0434	0.0768	0.1508	0.2394	0.7033	94.6401	49.8844	-2.7236
11	7.4675	-1.6293	-1.003	3.6277	0.3095	2.7479	0.2313	0.9	0.5637	-0.3005	-0.0616	-0.3008	-0.2102	0.152	-0.1697	0.0585	-0.0178	0.0574	0.5059	-0.2128	0.3322	52.2432	-35.555	-5.0583
12	2.1157	0.6624	0.0173	2.6841	-0.1382	4.2326	0.1928	-0.1693	-0.2815	0.2339	-0.2398	-0.1799	0.462	0.0429	0.047	0.3695	0.1116	0.0189	0.503	0.1486	0.2338	117.9757	-7.0308	26.0309

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 265
2	X-RAY DIFFRACTION	2	B	4 - 265
3	X-RAY DIFFRACTION	3	C	4 - 265
4	X-RAY DIFFRACTION	4	D	4 - 265
5	X-RAY DIFFRACTION	5	E	4 - 265
6	X-RAY DIFFRACTION	6	F	4 - 265
7	X-RAY DIFFRACTION	7	G	4 - 265
8	X-RAY DIFFRACTION	8	H	4 - 265
9	X-RAY DIFFRACTION	9	I	4 - 265
10	X-RAY DIFFRACTION	10	J	4 - 265
11	X-RAY DIFFRACTION	11	K	4 - 265
12	X-RAY DIFFRACTION	12	L	4 - 265

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