PDB-5iuw: Crystal Structure of Indole-3-acetaldehyde Dehydrogenase in compl...

ID or keywords:

Entry

Database: PDB / ID: 5iuw

Title

Crystal Structure of Indole-3-acetaldehyde Dehydrogenase in complexed with NAD+ and IAA

Components

Aldehyde dehydrogenase family protein

Keywords

OXIDOREDUCTASE / Indole-3-acetaldehyde dehydrogenase / aldehyde dehydrogenase

Function / homology

Function and homology information

oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function

Biological species

Pseudomonas syringae pv. tomato (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.093 Å

Authors

Lee, S.G. / McClerklin, S. / Kunkel, B. / Jez, J.M.

Funding support

United States, 1items

Citation

Journal: PLoS Pathog. / Year: 2018
Title: Indole-3-acetaldehyde dehydrogenase-dependent auxin synthesis contributes to virulence of Pseudomonas syringae strain DC3000.
Authors: McClerklin, S.A. / Lee, S.G. / Harper, C.P. / Nwumeh, R. / Jez, J.M. / Kunkel, B.N.

History

Deposition	Mar 18, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2018	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5iuw.cif.gz	390.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5iuw.ent.gz	318.6 KB	Display	PDB format
PDBx/mmJSON format	5iuw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5iuw_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5iuw_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5iuw_validation.xml.gz	44.4 KB	Display
Data in CIF	5iuw_validation.cif.gz	66.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iu/5iuw ftp://data.pdbj.org/pub/pdb/validation_reports/iu/5iuw	HTTPS FTP

-
Related structure data

Related structure data	5iuuC 5iuvSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5gtl-d 4lih-2 6b4r-d 5tei-1 5iuv-1 4qf6-1 1o9j-d 4wj9-1 2xdr-d 7jwv-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #127 - Jul 2010 Crystallins similarity (7) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (7)

Deposited unit

A: Aldehyde dehydrogenase family protein

B: Aldehyde dehydrogenase family protein

hetero molecules

107 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aldehyde dehydrogenase family protein

B: Aldehyde dehydrogenase family protein

hetero molecules

A: Aldehyde dehydrogenase family protein

B: Aldehyde dehydrogenase family protein

hetero molecules

defined by author&software
214 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.799, 84.883, 166.938
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-1237- HOH

#1: Protein	Aldehyde dehydrogenase family protein Mass: 52779.824 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (strain DC3000) (bacteria) Strain: DC3000 / Gene: PSPTO_0092 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88BC5
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID Mass: 175.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₉NO₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 855 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.64 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 8% PEG8000, 100 mM Tris

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2015
Radiation	Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.09→45.83 Å / Num. obs: 68374 / % possible obs: 100 % / Redundancy: 5.7 % / R_sym value: 0.143 / Net I/σ(I): 12.8
Reflection shell	Resolution: 2.09→2.13 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.19 / % possible all: 100

-
Processing

Software

Name	Version	Classification
HKL-3000		data reduction
PHASER		phasing
PHENIX	1.9_1692	refinement
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IUV

5iuv

Resolution: 2.093→45.829 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.72

	R_factor	Num. reflection	% reflection
R_free	0.1894	2009	2.94 %
R_work	0.1505	-	-
obs	0.1517	68364	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.093→45.829 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7386	0	114	855	8355

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7654
X-RAY DIFFRACTION	f_angle_d	1.009	10426
X-RAY DIFFRACTION	f_dihedral_angle_d	12.708	2710
X-RAY DIFFRACTION	f_chiral_restr	0.039	1192
X-RAY DIFFRACTION	f_plane_restr	0.005	1344

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.0925-2.1449	0.2657	142	0.2049	4561	X-RAY DIFFRACTION	98
2.1449-2.2029	0.2025	138	0.1817	4694	X-RAY DIFFRACTION	100
2.2029-2.2677	0.2282	143	0.1782	4707	X-RAY DIFFRACTION	100
2.2677-2.3409	0.2529	138	0.1729	4689	X-RAY DIFFRACTION	100
2.3409-2.4245	0.2354	148	0.1703	4702	X-RAY DIFFRACTION	100
2.4245-2.5216	0.2112	139	0.1613	4688	X-RAY DIFFRACTION	100
2.5216-2.6364	0.2108	141	0.1568	4699	X-RAY DIFFRACTION	100
2.6364-2.7753	0.1709	139	0.1582	4732	X-RAY DIFFRACTION	100
2.7753-2.9492	0.2126	143	0.1546	4740	X-RAY DIFFRACTION	100
2.9492-3.1768	0.202	146	0.1535	4735	X-RAY DIFFRACTION	100
3.1768-3.4964	0.1649	141	0.1422	4756	X-RAY DIFFRACTION	100
3.4964-4.0021	0.1761	151	0.1299	4796	X-RAY DIFFRACTION	100
4.0021-5.0412	0.1519	146	0.1165	4841	X-RAY DIFFRACTION	100
5.0412-45.84	0.1631	154	0.1528	5015	X-RAY DIFFRACTION	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	0.1988	0.0407	0.109	0.0967	0.0488	0.1182	0.0383	-0.0405	0.0161	-0.0446	0.0204	-0.1485	-0.0175	0.1161	0.0045	0.1135	-0.0277	-0.0175	0.1959	-0.0235	0.192	120.2391	125.2426	190.4598
2	0.0925	0.0612	0.0486	0.3235	0.3685	0.7239	0.0467	-0.1154	0.095	0.2182	0.0731	0.0393	-0.0272	0.2937	0.4069	0.1146	0.0002	-0.0367	0.2217	-0.0461	0.1134	108.7424	134.9338	198.0529
3	0.1517	-0.0527	0.1787	0.0732	0.0498	0.0983	0.0245	-0.0149	-0.0616	-0.0127	-0.0094	-0.0284	-0.0561	0.0764	-0	0.1154	-0.0199	0.0003	0.1266	-0.0056	0.1264	109.628	126.8391	180.8169
4	0.047	0.0487	0.0361	0.1306	0.1464	0.0558	-0.0196	-0.1169	0.077	0.0328	0.0356	-0.018	-0.0305	-0.0118	-0	0.1202	0.0016	0.0057	0.1256	0.0071	0.1224	90.214	133.5538	171.0266
5	0.3001	0.0417	-0.0448	0.0741	0.117	0.0749	0.0429	-0.0704	-0.0264	-0.0215	0.0043	-0.0134	-0.0329	0.0625	0.0001	0.1008	-0.0194	-0.0065	0.1329	-0.0071	0.1095	101.94	131.7142	190.4467
6	0.1268	0.1486	0.0451	0.0886	0.0056	0.0241	0.0253	-0.0848	0.0075	0.0068	-0.0152	0.0704	0.0571	0.0093	0.0071	0.1503	-0.0201	-0.0137	0.1321	-0.0039	0.1418	88.0849	120.2947	192.5718
7	0.1215	-0.0023	0.0598	0.053	0.1495	0.3902	0.063	-0.014	-0.1196	0.0336	0	-0.0621	0.031	0.1096	0.0214	0.2268	-0.0102	-0.0674	0.1282	0.0415	0.2257	96.173	97.9702	188.9483
8	0.118	0.1146	-0.1189	0.1392	0.0053	0.1247	0.0509	-0.2764	0.0252	0.0306	-0.0094	-0.0248	0.0289	0.1315	0.0226	0.2006	-0.0233	-0.0415	0.2393	0.0485	0.2207	105.5984	106.4709	200.1655
9	0.02	-0.0556	-0.126	0.1872	0.1671	0.2387	-0.1423	-0.2615	0.0548	0.1768	0.1523	-0.0896	0.2397	0.2239	0.0128	0.2609	-0.0065	-0.063	0.3425	0.0478	0.2383	101.459	99.878	201.8482
10	0.1301	-0.1322	0.0138	0.3374	0.0468	0.2312	0.0609	-0.1203	-0.076	0.127	-0.0823	0.009	0.103	-0.1135	-0.0147	0.1568	-0.0359	-0.0142	0.1233	0.0329	0.1395	85.0275	104.4999	188.4455
11	0.0641	-0.0543	-0.0951	0.0923	-0.0613	0.0822	0.0248	-0.0283	0.0022	-0.0364	-0.0038	-0.0401	0.0082	0.023	-0	0.1421	-0.0138	-0.0104	0.1307	0.0089	0.1259	87.8819	125.9427	179.5574
12	0.2104	0.0285	-0.0752	0.0272	-0.0011	0.0792	0.0292	-0.073	0.0852	-0.1094	0.0281	0.0761	0.0676	-0.1537	-0.0067	0.1177	-0.0131	0.0125	0.2134	-0.0058	0.1725	45.7126	135.7846	188.9336
13	0.2027	0.1228	-0.0694	0.1704	-0.16	0.7501	0.0731	-0.1918	-0.094	0.1068	-0.0162	-0.0467	0.0119	-0.2775	0.1717	0.0928	0.0036	0.0175	0.2192	-0.0008	0.0944	57.2305	128.632	198.9331
14	0.297	0.0214	-0.0149	0.022	0.1633	0.1278	0.0445	0.0365	0.0427	-0.0491	-0.0746	0.0936	0.0299	-0.0945	0	0.1322	-0.0041	0.0078	0.1229	0.0056	0.1359	56.3274	131.5682	180.098
15	0.2506	0.0576	-0.115	0.0332	0.0751	0.2394	0.0343	-0.0205	0.0518	-0.025	-0.033	-0.0152	-0.0033	-0.0409	0.0001	0.1065	-0.0092	0.0115	0.1067	-0.0022	0.1091	67.8652	127.4423	181.2609
16	0.2565	0.2034	-0.0288	0.2601	0.1083	0.2209	0.04	-0.1217	0.0509	-0.0233	-0.0412	-0.0427	-0.0037	-0.0188	-0.0228	0.0846	-0.006	0.0077	0.1213	-0.0215	0.104	72.9083	134.6535	192.4017
17	0.3609	-0.0297	-0.0016	-0.0971	0.0203	0.0513	0.0409	-0.1949	0.0679	0.0647	-0.0225	0.0412	-0.1291	-0.0977	0.0026	0.2961	0.0061	0.0644	0.2135	-0.03	0.2469	65.6565	159.2637	185.7381
18	0.2013	-0.167	0.3573	0.1338	-0.09	0.4314	0.0268	-0.1786	0.0352	0.1616	0.0163	-0.0031	-0.3435	-0.083	0.0123	0.3315	-0.0145	0.0553	0.2092	-0.0503	0.219	71.4991	161.2156	190.2122
19	0.0927	-0.0882	0.0426	0.1157	-0.0229	0.0254	0.0189	-0.0644	0.013	-0.0099	0.004	0.0368	-0.0009	0.011	0	0.145	-0.0084	0.01	0.1176	-0.0152	0.1252	79.9035	140.4294	177.7345

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 72 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 73 through 119 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 120 through 157 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 158 through 245 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 246 through 282 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 283 through 328 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 329 through 363 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 364 through 395 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 396 through 455 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 456 through 497 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 3 through 29 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 30 through 72 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 73 through 119 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 120 through 210 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 211 through 282 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 283 through 363 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 364 through 422 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 423 through 497 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi