PDB-1xmb: X-ray structure of IAA-aminoacid hydrolase from Arabidopsis thali...

ID or keywords:

Entry

Database: PDB / ID: 1xmb

Title

X-ray structure of IAA-aminoacid hydrolase from Arabidopsis thaliana gene AT5G56660

Components

IAA-amino acid hydrolase homolog 2

Keywords

HYDROLASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / AT5G56660 / ILL2 / indole-3-acetic acid / auxin / Center for Eukaryotic Structural Genomics

Function / homology

Function and homology information

IAA-amino acid conjugate hydrolase activity / IAA-Ala conjugate hydrolase activity / auxin metabolic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / endoplasmic reticulum lumen / endoplasmic reticulum / metal ion binding
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Wesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: Proteins / Year: 2009
Title: X-ray structure of ILL2, an auxin-conjugate amidohydrolase from Arabidopsis thaliana.
Authors: Bitto, E. / Bingman, C.A. / Bittova, L. / Houston, N.L. / Boston, R.S. / Fox, B.G. / Phillips Jr., G.N.

History

Deposition	Oct 1, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2004	Provider: repository / Type: Initial release
Revision 1.1	Feb 4, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jan 30, 2013	Group: Database references / Structure summary
Revision 1.4	Oct 11, 2017	Group: Refinement description / Category: software
Revision 1.5	Feb 14, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1xmb.cif.gz	94.1 KB	Display	PDBx/mmCIF format
PDB format	pdb1xmb.ent.gz	69.2 KB	Display	PDB format
PDBx/mmJSON format	1xmb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	1xmb_validation.pdf.gz	421 KB	Display	wwPDB validaton report
Full document	1xmb_full_validation.pdf.gz	423.6 KB	Display
Data in XML	1xmb_validation.xml.gz	18.3 KB	Display
Data in CIF	1xmb_validation.cif.gz	27.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xm/1xmb ftp://data.pdbj.org/pub/pdb/validation_reports/xm/1xmb	HTTPS FTP

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Related structure data

Similar structure data	4i1r-d 6yn9-d 5zql-2 4prx-d 4esj-1 6ed6-2 6p5p-3 1bob-d 2q43-d 6vo5-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.22207

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (11) #108 - Dec 2008 Hsp90 similarity (1)

Deposited unit

A: IAA-amino acid hydrolase homolog 2

45.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	75.264, 75.264, 130.880
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	IAA-amino acid hydrolase homolog 2 Mass: 45567.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ILL2 / Plasmid: pVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) p(LacI+RARE) / References: UniProt: P54970
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.62 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 10 mg/mL PROTEIN, 0.080 M MAGNESIUM SULFATE, 14 % PEG 1500, 0.100 M CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	110	1
2	110	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	19-BM	1	0.96411
SYNCHROTRON	APS	19-BM	2	0.97932

Detector

Type	ID	Detector	Date	Details
APS-1	1	CCD	Aug 1, 2004	Rosenbaum-Rock vertical focusing mirror
APS-1	2	CCD	Jul 30, 2004	Rosenbaum-Rock vertical focusing mirror

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Rosenbaum-Rock double-crystal monochromator: water cooled, sagitally focusing 2nd crystal	SINGLE WAVELENGTH	M	x-ray	1
2	Rosenbaum-Rock double-crystal monochromator: water cooled, sagitally focusing 2nd crystal	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.96411	1
2	0.97932	1

Reflection

Resolution: 2→24.21 Å / Num. obs: 29672 / % possible obs: 99.9 % / Redundancy: 8.4 % / R_merge(I) obs: 0.043 / Χ²: 0.432 / Net I/σ(I): 22

Reflection shell

Diffraction-ID: 1,2

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Χ²	% possible all
2-2.07	6.3	0.334	3.8	2939	0.491	99.9
2.07-2.15		0.212		2907	0.348	100
2.15-2.25		0.158		2935	0.371	100
2.25-2.37		0.12		2925	0.379	100
2.37-2.52		0.095		2940	0.391	100
2.52-2.71		0.069		2945	0.401	100
2.71-2.99		0.05		2953	0.419	100
2.99-3.42		0.035		2986	0.45	100
3.42-4.31		0.027		3010	0.511	100
4.31-50		0.024		3132	0.575	98.8

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 2.001 Å / D res low: 15 Å / FOM : 0.35 / Reflection: 28286

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	44.286	9.772	11.437	SE	20.1	0.56
2	40.529	26.843	6.218	SE	16.7	0.54
3	37.354	28.705	11.632	SE	26.8	0.62
4	46.419	30.525	2.999	SE	26.8	0.53
5	57.929	28.818	8.217	SE	28.1	0.68
6	46.712	16.036	15.583	SE	38.8	0.71
7	0.404	36.131	0.847	SE	20.6	0.4
8	-15.654	55.461	11.185	SE	42.3	0.51
9	-17.767	49.567	0.78	SE	46.7	0.52

Phasing MAD shell

Resolution (Å)	FOM	Reflection
6.75-15	0.45	1608
4.42-6.75	0.41	2512
3.5-4.42	0.44	3132
2.99-3.5	0.46	3590
2.65-2.99	0.41	4013
2.4-2.65	0.35	4311
2.21-2.4	0.25	4507
2.06-2.21	0.18	4613

Phasing dm

FOM : 0.64 / FOM acentric: 0.64 / FOM centric: 0.61 / Reflection: 28287 / Reflection acentric: 25455 / Reflection centric: 2832

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5.7-14.984	0.93	0.93	0.81	1302	969	333
3.6-5.7	0.91	0.93	0.82	4034	3423	611
2.9-3.6	0.82	0.84	0.68	4928	4387	541
2.5-2.9	0.69	0.7	0.55	4895	4446	449
2.1-2.5	0.52	0.53	0.45	8285	7680	605
2-2.1	0.32	0.33	0.27	4843	4550	293

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.06	phasing
ARP/wARP	2.06	model building
RESOLVE	2.06	phasing
REFMAC	refmac_5.2.0005	refinement

Refinement

Method to determine structure:

SAD / Resolution: 2→24.21 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.947 / WR_factor R_free: 0.197 / WR_factor R_work: 0.153 / SU B: 3.155 / SU ML: 0.09 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2039	1504	5.076 %	RANDOM
R_work	0.1567	-	-	-
all	0.159	-	-	-
obs	0.159	29630	99.821 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 27.747 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.005 Å²	-0.003 Å²	0 Å²
2-	-	-0.005 Å²	0 Å²
3-	-	-	0.008 Å²

Refinement step

Cycle: LAST / Resolution: 2→24.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2889	0	0	285	3174

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	2954
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2738
X-RAY DIFFRACTION	r_angle_refined_deg	1.587	1.964	3993
X-RAY DIFFRACTION	r_angle_other_deg	0.838	3	6384
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.279	5	372
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.503	24.113	124
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.355	15	516
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.747	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	452
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3259
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	571
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	604
X-RAY DIFFRACTION	r_nbd_other	0.189	0.2	2665
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1442
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	1687
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.252	0.2	222
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.197	0.2	8
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.279	0.2	46
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.261	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	2.193	2	2385
X-RAY DIFFRACTION	r_mcbond_other	0.353	2	764
X-RAY DIFFRACTION	r_mcangle_it	2.872	4	2997
X-RAY DIFFRACTION	r_mcangle_other	1.339	4	2563
X-RAY DIFFRACTION	r_scbond_it	5.454	6	1249
X-RAY DIFFRACTION	r_scbond_other	1.828	6	2316
X-RAY DIFFRACTION	r_scangle_it	7.081	8	996
X-RAY DIFFRACTION	r_scangle_other	3.065	8	3821

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.052	0.247	110	0.186	2058	2181	99.404
2.052-2.108	0.251	97	0.168	1984	2081	100
2.108-2.169	0.2	115	0.162	1942	2057	100
2.169-2.236	0.219	105	0.16	1872	1977	100
2.236-2.309	0.192	96	0.154	1834	1930	100
2.309-2.39	0.208	115	0.158	1760	1875	100
2.39-2.48	0.201	104	0.156	1708	1812	100
2.48-2.581	0.161	85	0.157	1653	1738	100
2.581-2.696	0.216	88	0.163	1598	1686	100
2.696-2.827	0.268	75	0.164	1519	1594	100
2.827-2.98	0.218	74	0.161	1471	1545	100
2.98-3.16	0.241	69	0.154	1375	1444	100
3.16-3.378	0.223	66	0.149	1297	1363	100
3.378-3.648	0.208	63	0.146	1214	1277	100
3.648-3.995	0.193	57	0.136	1139	1196	100
3.995-4.464	0.152	51	0.135	1021	1072	100
4.464-5.151	0.166	44	0.144	914	959	99.896
5.151-6.299	0.183	44	0.181	791	835	100
6.299-8.866	0.213	31	0.189	627	658	100
8.866-65.233	0.219	15	0.192	349	403	90.323

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