PDB-6u60: Crystal structure of prephenate dehydrogenase tyrA from Bacillus ...

ID or keywords:

Entry

Database: PDB / ID: 6u60

Title

Crystal structure of prephenate dehydrogenase tyrA from Bacillus anthracis in complex with NAD and L-tyrosine

Components

Prephenate dehydrogenase

Keywords

HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

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

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Shabalin, I.G. / Hou, J. / Kutner, J. / Grimshaw, S. / Christendat, D. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: Febs J. / Year: 2020
Title: Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain.
Authors: Shabalin, I.G. / Gritsunov, A. / Hou, J. / Slawek, J. / Miks, C.D. / Cooper, D.R. / Minor, W. / Christendat, D.

History

Deposition	Aug 28, 2019	Deposition site: RCSB / Processing site: RCSB
Supersession	Sep 11, 2019	ID: 5USC
Revision 1.0	Sep 11, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Apr 7, 2021	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 1.3	Oct 11, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6u60.cif.gz	309.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6u60.ent.gz	248.8 KB	Display	PDB format
PDBx/mmJSON format	6u60.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6u60_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	6u60_full_validation.pdf.gz	1.2 MB	Display
Data in XML	6u60_validation.xml.gz	30.3 KB	Display
Data in CIF	6u60_validation.cif.gz	44.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u6/6u60 ftp://data.pdbj.org/pub/pdb/validation_reports/u6/6u60	HTTPS FTP

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Related structure data

Related structure data	5uyyC 5v0sC 6cxdC 3gggS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3hno-1 3hno-2 4e5p-3 2cuk-1 2v5p-1 6iwt-d 3hno-3 1kyw-1 6i70-d 1nx6-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18430/M35USC / Data set type: diffraction image data
Other databases	TargetTrack: CSGID-IDP05722

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#61 - Jan 2005 Phenylalanine Hydroxylase similarity (2) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (2) #22 - Oct 2001 Photosystem I similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #127 - Jul 2010 Crystallins similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Prephenate dehydrogenase

B: Prephenate dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	106.850, 81.003, 83.597
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 14 - 378 / Label seq-ID: 17 - 381

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	Prephenate dehydrogenase Mass: 42707.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: tyrA, GBAA_2954 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81P63, prephenate dehydrogenase
#2: Chemical	ChemComp-TYR / TYROSINE Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₁NO₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.22 Å³/Da / Density % sol: 44.52 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion / pH: 6.2 Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, 10 mM BME, 5 mM NAD and 20 mM Tyrosine were mixed with 0.2 ul of the MCSG Suite 2 condition #81 (0.1 M ...Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, 10 mM BME, 5 mM NAD and 20 mM Tyrosine were mixed with 0.2 ul of the MCSG Suite 2 condition #81 (0.1 M Potassium/Sodium phosphate pH=6.2, 0.2M Sodium chloride, 20% w/v PEG 1000) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization the protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours

Crystal

Density Matthews: 2.22 Å³/Da / Density % sol: 44.52 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion / pH: 6.2
Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, 10 mM BME, 5 mM NAD and 20 mM Tyrosine were mixed with 0.2 ul of the MCSG Suite 2 condition #81 (0.1 M ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2015 / Details: Beryllium Lenses

Radiation

Monochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 42991 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / B_iso Wilson estimate: 24.8 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.027 / R_rim(I) all: 0.08 / Χ²: 0.965 / Net I/av σ(I): 27.8 / Net I/σ(I): 9.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.1-2.14	6.7	1.302	1.6	2137	0.612	0.534	1.411	0.954	99.3
2.14-2.18	7.2	0.976		2066	0.742	0.383	1.051	0.87	99.3
2.18-2.22	7.8	0.826		2104	0.803	0.311	0.884	0.896	99.6
2.22-2.26	8.2	0.737		2138	0.849	0.268	0.785	0.863	99.7
2.26-2.31	8.3	0.653		2117	0.899	0.237	0.695	0.896	99.8
2.31-2.37	8.4	0.531		2110	0.924	0.192	0.566	0.844	99.9
2.37-2.42	8.4	0.434		2139	0.946	0.157	0.462	0.876	99.9
2.42-2.49	8.5	0.362		2132	0.964	0.131	0.385	0.864	99.9
2.49-2.56	8.6	0.31		2103	0.971	0.112	0.33	0.891	100
2.56-2.65	8.6	0.239		2156	0.982	0.086	0.255	0.87	100
2.65-2.74	8.7	0.195		2124	0.989	0.07	0.208	0.906	100
2.74-2.85	8.9	0.152		2142	0.992	0.054	0.161	0.949	100
2.85-2.98	9	0.121		2163	0.995	0.043	0.128	0.979	100
2.98-3.14	9.1	0.093		2138	0.995	0.033	0.099	0.998	100
3.14-3.33	9.1	0.068		2155	0.997	0.024	0.072	1.018	100
3.33-3.59	9	0.054		2156	0.998	0.019	0.058	1.072	100
3.59-3.95	9	0.048		2184	0.998	0.017	0.051	1.229	100
3.95-4.52	8.9	0.045		2189	0.997	0.016	0.048	1.367	100
4.52-5.7	8.8	0.036		2216	0.999	0.013	0.038	0.993	100
5.7-50	8.1	0.034		2322	0.998	0.013	0.037	0.867	99.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
HKL-3000		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
MOLREP		phasing
Coot		model building
HKL-3000		phasing
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3GGG

3ggg

Resolution: 2.1→36.48 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.936 / WR_factor R_free: 0.2086 / WR_factor R_work: 0.1511 / FOM work R set: 0.8284 / SU B: 11.542 / SU ML: 0.151 / SU R Cruickshank DPI: 0.2356 / SU R_free: 0.1931 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2203	1975	4.9 %	RANDOM
R_work	0.1605	-	-	-
obs	0.1634	38244	93.44 %	-

Solvent computation

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

Displacement parameters

B_iso max: 176.42 Å² / B_iso mean: 36.389 Å² / B_iso min: 6.31 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.59 Å²	-0 Å²	-0 Å²
2-	-	-0.2 Å²	0 Å²
3-	-	-	0.8 Å²

Refinement step

Cycle: final / Resolution: 2.1→36.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5703	0	80	370	6153
B_iso mean	-	-	25.7	36.04	-
Num. residues	-	-	-	-	730

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	5897
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	5509
X-RAY DIFFRACTION	r_angle_refined_deg	1.484	1.631	7985
X-RAY DIFFRACTION	r_angle_other_deg	1.352	1.582	12779
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.281	5	728
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.322	23.287	286
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.419	15	1037
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.163	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	777
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6633
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1162

Refine LS restraints NCS

Ens-ID: 1 / Number: 10460 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.101→2.155 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.258	95	-
R_work	0.234	1839	-
all	-	1934	-
obs	-	-	61.28 %

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	7.1624	-2.2534	1.14	3.7095	-1.5459	5.356	-0.0325	0.5757	0.9529	-0.3149	0.016	0.1902	-0.4431	-0.322	0.0165	0.2282	0.0566	-0.1472	0.2008	0.1137	0.2747	50.458	24.607	9.696
2	4.7727	-0.8305	0.3057	1.3887	-0.8932	6.6873	0.0189	-0.2797	0.5002	-0.0212	0.0635	0.3758	-0.6175	-0.7517	-0.0823	0.1456	0.0823	-0.042	0.2881	-0.0218	0.2386	46.552	20.734	24.61
3	6.605	0.7877	-1.1732	2.1026	-0.7663	4.6689	-0.0437	-0.0944	0.0339	-0.0536	0.0667	0.2316	0.0715	-0.1946	-0.0231	0.1325	0.0264	-0.0534	0.127	-0.0064	0.0445	56.865	12.52	18.498
4	13.534	10.0839	0.9322	9.4454	0.459	1.5157	0.1877	-0.0147	-0.0961	0.2359	-0.0077	-0.1691	-0.1177	-0.0975	-0.1799	0.0754	0.0411	0.002	0.1465	0.0058	0.0307	75.501	21.656	32.76
5	3.0787	0.3121	0.0815	0.8595	-0.096	1.5104	0.0398	-0.1763	0.0944	0.1096	-0.0017	0.0159	-0.2296	-0.0788	-0.0381	0.0868	0.0033	-0.0082	0.1038	-0.0126	0.0118	80.594	23.128	34.231
6	16.1695	5.3675	10.6933	5.1417	4.9758	13.0653	0.3911	-0.4908	-0.6868	0.1651	-0.1984	-0.2491	0.5951	-0.5321	-0.1927	0.1756	-0.0015	-0.0192	0.0651	0.0094	0.0986	87.214	6.336	28.612
7	3.3613	1.1187	0.4318	4.4333	-0.1766	2.9545	0.0208	-0.1001	-0.3992	-0.0526	0.0196	-0.2071	0.3454	-0.1369	-0.0405	0.2045	-0.0194	-0.0268	0.0295	-0.0113	0.0776	82.95	0.098	7.173
8	3.4662	0.7022	-0.1958	2.7499	1.3593	3.2121	0.0366	0.3183	-0.2548	-0.1972	0.1131	-0.1274	0.0851	0.2899	-0.1498	0.1585	-0.0003	0.009	0.1177	-0.0417	0.1604	116.335	16.263	15.099
9	9.2598	-1.2745	2.594	15.6746	-6.2865	9.9372	0.2092	-0.2773	-0.2447	0.6486	0.1581	-0.363	-0.0585	0.8167	-0.3674	0.1373	0.0099	0.0183	0.269	-0.1177	0.1881	126.357	21.045	25.072
10	3.7401	0.4769	0.5764	0.8729	0.2309	2.2254	-0.0029	0.0161	0.188	-0.0792	0.0746	-0.0587	-0.2158	0.2554	-0.0717	0.1392	-0.0412	0.013	0.0493	0.0094	0.0797	110.173	27.686	22.505
11	5.2955	2.6403	0.3216	3.0028	0.2308	1.2817	-0.0061	0.1339	-0.0656	-0.057	0.0482	0.1458	0.0636	-0.1242	-0.0422	0.0846	0.0035	-0.0062	0.1198	0.0126	0.0362	87.242	15.413	29.855
12	2.8265	-0.0899	0.0864	0.9546	-0.2432	2.1072	0.086	-0.2752	0.397	0.0942	-0.0277	0.1291	-0.3023	-0.1606	-0.0583	0.1287	-0.0065	0.0218	0.0925	-0.0327	0.1033	81.827	28.76	36.302
13	2.106	1.8153	1.6673	3.5616	2.332	3.2305	-0.0094	-0.0548	0.0054	-0.2315	-0.0371	0.0003	-0.0549	-0.0882	0.0465	0.1661	-0.0208	0.0117	0.0863	0.0273	0.0132	81.364	18.349	8.225
14	3.8198	1.5166	-0.2842	2.3415	-0.2869	2.2826	-0.0289	-0.1147	0.2074	-0.2002	0.0038	0.021	-0.1802	0.0438	0.0251	0.1822	-0.0123	-0.0016	0.0289	-0.0033	0.0147	81.565	20.405	6.338

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	14 - 64
2	X-RAY DIFFRACTION	2	A	65 - 122
3	X-RAY DIFFRACTION	3	A	123 - 186
4	X-RAY DIFFRACTION	4	A	187 - 217
5	X-RAY DIFFRACTION	5	A	218 - 278
6	X-RAY DIFFRACTION	6	A	279 - 299
7	X-RAY DIFFRACTION	7	A	300 - 378
8	X-RAY DIFFRACTION	8	B	14 - 90
9	X-RAY DIFFRACTION	9	B	91 - 102
10	X-RAY DIFFRACTION	10	B	103 - 188
11	X-RAY DIFFRACTION	11	B	189 - 249
12	X-RAY DIFFRACTION	12	B	250 - 298
13	X-RAY DIFFRACTION	13	B	299 - 325
14	X-RAY DIFFRACTION	14	B	326 - 378

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