PDB-5t9e: Seleno-methionine Prephenate Dehydrogenase from Soybean

ID or keywords:

Entry

Database: PDB / ID: 5t9e

Title

Seleno-methionine Prephenate Dehydrogenase from Soybean

Components

Prephenate dehydrogenase 1

Keywords

OXIDOREDUCTASE / dehydrogenase / tyrosine biosynthesis

Function / homology

Function and homology information

prephenate dehydrogenase (NADP+) / arogenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process / NAD+ binding
Similarity search - Function

Biological species

Glycine max (soybean)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.03 Å

Authors

Holland, C.K. / Jez, J.M. / Lee, S.G.

Funding support

United States, 1items

Citation

Journal: Nat. Chem. Biol. / Year: 2017
Title: Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants.
Authors: Schenck, C.A. / Holland, C.K. / Schneider, M.R. / Men, Y. / Lee, S.G. / Jez, J.M. / Maeda, H.A.

History

Deposition	Sep 9, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 28, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 19, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Aug 30, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Sep 27, 2017	Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.4	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5t9e.cif.gz	213.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5t9e.ent.gz	180.6 KB	Display	PDB format
PDBx/mmJSON format	5t9e.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5t9e_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5t9e_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5t9e_validation.xml.gz	23.2 KB	Display
Data in CIF	5t9e_validation.cif.gz	32.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t9/5t9e ftp://data.pdbj.org/pub/pdb/validation_reports/t9/5t9e	HTTPS FTP

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Related structure data

Related structure data	5t95C 5t9fC 5whxC C: citing same article (ref.)
Similar structure data	5whx-d 5t9f-2 5t95-d 1l8l-d 6eo2-1 4op0-d 6kbb-d 6t5z-d 6bvz-d 4exb-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #127 - Jul 2010 Crystallins similarity (1)

Deposited unit

A: Prephenate dehydrogenase 1

B: Prephenate dehydrogenase 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	46.508, 55.127, 68.592
Angle α, β, γ (deg.)	107.34, 98.89, 103.55
Int Tables number	1
Space group name H-M	P1

#1: Protein	Prephenate dehydrogenase 1 / Uncharacterized protein Mass: 31244.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Gene: PDH1, GLYMA_18G023100 / Cell (production host): Rosetta 2 / Production host: Escherichia coli (E. coli) References: UniProt: I1MYY4, prephenate dehydrogenase (NADP+)
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.34 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 20% (w/v) PEG-3350, 100 mM sodium citrate, pH 4.0, and 200 mM sodium citrate tribasic

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.03→35 Å / Num. obs: 60106 / % possible obs: 96 % / Redundancy: 1.8 % / R_merge(I) obs: 0.068 / R_sym value: 0.061 / Net I/σ(I): 7.6
Reflection shell	Resolution: 2→2.03 Å / R_merge(I) obs: 0.328 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1687 / % possible all: 88.7

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data collection
MLPHARE		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.03→34.06 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.79
Details: The reason of the low completeness (60%) is the low anomalous completeness

	R_factor	Num. reflection	% reflection
R_free	0.229	3037	6.02 %
R_work	0.188	-	-
obs	0.19	50450	63.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.03→34.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3970	0	96	222	4288

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4201
X-RAY DIFFRACTION	f_angle_d	1.172	5694
X-RAY DIFFRACTION	f_dihedral_angle_d	14.536	1540
X-RAY DIFFRACTION	f_chiral_restr	0.046	657
X-RAY DIFFRACTION	f_plane_restr	0.004	710

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 (%)
2.0271-2.0588	0.2408	24	0.2471	363	X-RAY DIFFRACTION	11
2.0588-2.0926	0.3347	64	0.214	1011	X-RAY DIFFRACTION	31
2.0926-2.1286	0.2236	76	0.2104	1174	X-RAY DIFFRACTION	34
2.1286-2.1673	0.2671	79	0.2065	1295	X-RAY DIFFRACTION	38
2.1673-2.209	0.2679	94	0.1977	1493	X-RAY DIFFRACTION	44
2.209-2.2541	0.2614	98	0.2038	1594	X-RAY DIFFRACTION	47
2.2541-2.3031	0.2428	110	0.1985	1767	X-RAY DIFFRACTION	52
2.3031-2.3567	0.2417	127	0.214	1859	X-RAY DIFFRACTION	55
2.3567-2.4156	0.2286	129	0.2045	2057	X-RAY DIFFRACTION	60
2.4156-2.4809	0.2504	139	0.2044	2168	X-RAY DIFFRACTION	63
2.4809-2.5539	0.2517	148	0.2067	2247	X-RAY DIFFRACTION	66
2.5539-2.6363	0.2782	150	0.2087	2426	X-RAY DIFFRACTION	71
2.6363-2.7305	0.2526	161	0.2078	2455	X-RAY DIFFRACTION	73
2.7305-2.8397	0.2344	166	0.2055	2584	X-RAY DIFFRACTION	76
2.8397-2.9689	0.2414	161	0.211	2654	X-RAY DIFFRACTION	78
2.9689-3.1253	0.2805	179	0.1924	2778	X-RAY DIFFRACTION	82
3.1253-3.321	0.2417	188	0.1825	2833	X-RAY DIFFRACTION	83
3.321-3.5771	0.2113	186	0.1769	2844	X-RAY DIFFRACTION	84
3.5771-3.9366	0.199	183	0.1651	2869	X-RAY DIFFRACTION	84
3.9366-4.5052	0.1926	182	0.1582	2895	X-RAY DIFFRACTION	86
4.5052-5.6718	0.2389	195	0.1734	3040	X-RAY DIFFRACTION	89
5.6718-34.066	0.197	198	0.2005	3007	X-RAY DIFFRACTION	89

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	0.3833	-0.4816	0.1396	0.6581	-0.0686	0.7869	-0.0266	-0.0289	-0.003	0.1019	0.0249	-0.0824	0.0392	-0.0054	-0	0.1427	-0.0053	0.015	0.1045	0.0081	0.127	49.0753	11.3856	23.6289
2	0.1378	-0.0161	-0.1544	0.1915	-0.3499	0.1771	-0.0205	0.0512	-0.0335	-0.0811	0.011	0.1367	0.0025	-0.1128	0	0.1738	-0.0037	-0.0014	0.1299	-0.0073	0.1289	46.8877	35.8117	9.0716
3	-0.0154	-0.0807	0.0013	0.022	0.0405	0.014	0.2247	0.0961	0.1666	0.1384	-0.162	-0.0136	0.1425	0.1363	-0.0016	0.1517	-0.0154	-0.0353	0.2248	0.001	0.2272	43.4858	-1.0734	-7.3237
4	0.2227	0.0736	-0.2087	0.0144	-0.0704	0.3101	-0.1479	-0.1142	-0.2141	-0.0617	-0.0311	-0.2827	0.0722	0.2391	-0.0378	0.0916	-0.0248	-0.0317	0.1292	-0.0061	0.1805	45.0374	9.4555	-2.8898
5	0.0176	-0.0497	-0.0541	0.0358	-0.0286	0.0043	0.0927	0.0699	-0.0547	-0.072	-0.1246	0.0782	-0.301	-0.0051	-0.0005	0.1398	0.034	0.0174	0.1551	0.0152	0.1453	33.8629	7.0424	-9.8783
6	0.2826	-0.0096	0.3431	0.2421	0.0374	0.3225	-0.0149	-0.075	0.396	0.0097	0.1956	0.1128	-0.3512	-0.0993	0.0008	0.1994	-0.0019	0.0199	0.1422	0.0126	0.176	30.6997	5.8017	-16.3654
7	0.295	-0.2133	-0.3914	0.6304	-0.1546	0.9172	0.196	0.0219	-0.066	0.3668	-0.3261	0.575	0.1989	-0.4363	-0.067	0.2629	-0.0524	-0.013	0.1478	0.0067	0.1681	36.0089	-13.5331	-2.7259
8	0.1581	-0.0083	0.2395	0.1511	0.0348	0.1769	-0.075	0.3371	-0.3769	0.2181	-0.0063	0.2713	0.1613	-0.3451	-0.014	0.1485	-0.0187	0.0102	0.2431	-0.0083	0.1543	35.7753	-6.2601	-19.2053
9	0.1055	-0.0085	-0.0831	0.0889	-0.1202	0.3577	-0.0544	0.1496	-0.2674	-0.1269	0.1195	-0.2804	0.2535	-0.0615	0.0123	0.1884	0.0095	-0.0445	0.1572	-0.0732	0.2691	23.372	-10.6756	-12.8164
10	-0.0163	-0.1007	0.0331	0.6355	-0.4156	0.2169	-0.0157	0.0362	0.3837	0.5521	0.1854	0.0914	-0.5022	-0.0106	-0.0006	0.1697	-0.0006	-0.0439	0.205	-0.037	0.1617	21.4113	-13.1626	12.4297
11	0.6233	0.124	-0.3072	0.2062	0.3911	1.2318	0.0551	-0.1747	0.3661	-0.2456	0.0003	0.0403	-0.6614	0.1426	0.0326	0.0773	-0.004	-0.025	0.1974	0.0091	0.1464	26.4969	-15.0215	10.7653
12	0.0377	-0.0485	-0.0608	0.0826	0.1182	0.2199	0.2236	-0.0295	-0.0914	-0.1869	0.0014	-0.2336	-0.2918	-0.2617	0.0393	0.1286	0.0144	-0.0348	0.1722	-0.0172	0.2303	20.111	-0.6432	-1.2195
13	0.1355	0.2207	-0.1032	0.3601	-0.009	0.7613	0.2251	-0.0161	0.0652	0.1175	0.0705	0.6165	-0.3376	-0.2682	0.0018	0.0851	0.0019	-0.002	0.2195	0.0471	0.2236	4.5476	-14.1828	6.505

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 9 THROUGH 183 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 184 THROUGH 258 )
3	X-RAY DIFFRACTION	3	CHAIN 'B' AND (RESID 9 THROUGH 38 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 39 THROUGH 63 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 64 THROUGH 83 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 84 THROUGH 125 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 126 THROUGH 139 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 140 THROUGH 164 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 165 THROUGH 183 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 184 THROUGH 206 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 207 THROUGH 221 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 222 THROUGH 236 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 237 THROUGH 258 )

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