PDB-2f1k: Crystal structure of Synechocystis arogenate dehydrogenase

ID or keywords:

Entry

Database: PDB / ID: 2f1k

Title

Crystal structure of Synechocystis arogenate dehydrogenase

Components

prephenate dehydrogenase

Keywords

OXIDOREDUCTASE / arogenate/prephenate dehydrogenase / tyrosine synthesis / X-ray crystallography structure

Function / homology

Function and homology information

prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process /

NAD+ binding / identical protein binding
Similarity search - Function

Biological species

Synechocystis sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.55 Å

Authors

Legrand, P. / Dumas, R. / Seux, M. / Rippert, P. / Ravelli, R. / Ferrer, J.-L. / Matringe, M.

Citation

Journal: Structure / Year: 2006
Title: Biochemical Characterization and Crystal Structure of Synechocystis Arogenate Dehydrogenase Provide Insights into Catalytic Reaction
Authors: Legrand, P. / Dumas, R. / Seux, M. / Rippert, P. / Ravelli, R. / Ferrer, J.-L. / Matringe, M.

History

Deposition	Nov 14, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 9, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2f1k.cif.gz	229.3 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	2f1k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f1/2f1k ftp://data.pdbj.org/pub/pdb/validation_reports/f1/2f1k	HTTPS FTP

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Related structure data

Similar structure data	2g5c-2 2g5c-1 3hlt-4 3ggg-2 4m1o-d 4odd-d 3dzb-d 4lyf-d 3d1l-d 3v71-d 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

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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

B: prephenate dehydrogenase

C: prephenate dehydrogenase

D: prephenate dehydrogenase

hetero molecules

125 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: prephenate dehydrogenase

B: prephenate dehydrogenase

hetero molecules

defined by author&software
62.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: prephenate dehydrogenase

D: prephenate dehydrogenase

hetero molecules

defined by author&software
62.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.150, 70.850, 104.490
Angle α, β, γ (deg.)	90.00, 90.30, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 5

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ILE	VAL	A	A	3 - 6	3 - 6
2	1	1	ILE	VAL	B	B	3 - 6	3 - 6
3	1	1	ILE	VAL	C	C	3 - 6	3 - 6
4	1	1	ILE	VAL	D	D	3 - 6	3 - 6
5	2	1	TYR	VAL	A	A	25 - 29	25 - 29
6	2	1	TYR	VAL	B	B	25 - 29	25 - 29
7	2	1	TYR	VAL	C	C	25 - 29	25 - 29
8	2	1	TYR	VAL	D	D	25 - 29	25 - 29
9	3	1	TYR	VAL	A	A	25 - 29	25 - 29
10	3	1	TYR	VAL	B	B	25 - 29	25 - 29
11	3	1	TYR	VAL	C	C	25 - 29	25 - 29
12	3	1	TYR	VAL	D	D	25 - 29	25 - 29
13	4	1	LYS	CYS	A	A	59 - 64	59 - 64
14	4	1	LYS	CYS	B	B	59 - 64	59 - 64
15	4	1	LYS	CYS	C	C	59 - 64	59 - 64
16	4	1	LYS	CYS	D	D	59 - 64	59 - 64
17	5	1	ALA	ALA	A	A	85 - 91	85 - 91
18	5	1	ALA	ALA	B	B	85 - 91	85 - 91
19	5	1	ALA	ALA	C	C	85 - 91	85 - 91
20	5	1	ALA	ALA	D	D	85 - 91	85 - 91
21	6	1	ILE	OMT	A	A	109 - 114	109 - 114
22	6	1	ILE	OMT	B	B	109 - 114	109 - 114
23	6	1	ILE	OMT	C	C	109 - 114	109 - 114
24	6	1	ILE	OMT	D	D	109 - 114	109 - 114
25	7	1	ALA	THR	A	A	133 - 138	133 - 138
26	7	1	ALA	THR	B	B	133 - 138	133 - 138
27	7	1	ALA	THR	C	C	133 - 138	133 - 138
28	7	1	ALA	THR	D	D	133 - 138	133 - 138
29	8	1	VAL	CYS	A	A	160 - 165	160 - 165
30	8	1	VAL	CYS	B	B	160 - 165	160 - 165
31	8	1	VAL	CYS	C	C	160 - 165	160 - 165
32	8	1	VAL	CYS	D	D	160 - 165	160 - 165
1	1	2	THR	LYS	A	A	166 - 276	166 - 276
2	1	2	THR	LYS	B	B	166 - 276	166 - 276
3	1	2	THR	LYS	C	C	166 - 276	166 - 276
4	1	2	THR	LYS	D	D	166 - 276	166 - 276

NCS ensembles :

ID
1
2

Details

two copies of the biological dimer are present in the assymetric units

#1: Protein	prephenate dehydrogenase / / arogenate dehydrogenase Mass: 30324.611 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: D90910.1 / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (lambda DE3) / References: UniProt: P73906, EC: 1.3.1.43
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.02 Å³/Da / Density % sol: 39.2 %
Crystal grow	Temperature: 294 K / pH: 8 Details: 1 uL prot + 1 uL reservoir (PEG 6000 30%, 0.1 M tris-HCl) + 2uL NADP 2 mM, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 8.00

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
1,2		1

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-4 / Wavelength: 1.072

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2003

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	DIAMOND	SINGLE WAVELENGTH	M	x-ray	1
2			M	x-ray	1

Radiation wavelength

Wavelength: 1.072 Å / Relative weight: 1

Reflection

Resolution: 1.55→20 Å / Num. obs: 135727 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.09 % / R_sym value: 0.046 / Net I/σ(I): 17.06

Reflection shell

Resolution: 1.55→1.61 Å / Redundancy: 3.46 % / Mean I/σ(I) obs: 3.01 / R_sym value: 0.426 / % possible all: 85.5

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
ProDC		data collection
XDS		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.55→20 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.946 / SU B: 3.55 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22191	6895	5 %	RANDOM
R_work	0.18863	-	-	-
obs	0.1903	131035	99.14 %	-
all	-	132172	-	-

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 mean: 17.34 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.12 Å²	0 Å²	0.01 Å²
2-	-	-0.07 Å²	0 Å²
3-	-	-	-0.04 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8498	0	208	424	9130

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	9012
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.665	2.012	12330
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.275	5	1136
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.564	24.819	359
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.118	15	1506
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.566	15	50
X-RAY DIFFRACTION	r_chiral_restr	0.15	0.2	1442
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6630
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	4622
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	6252
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	532
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.14	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.234	0.2	95
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.235	0.2	15
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.819	1.5	5787
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.23	2	9081
X-RAY DIFFRACTION	r_scbond_it	2.06	3	3610
X-RAY DIFFRACTION	r_scangle_it	3.099	4.5	3247
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	257	medium positional	0.14	0.3
1	2	B	257	medium positional	0.11	0.3
1	3	C	257	medium positional	0.15	0.3
1	4	D	257	medium positional	0.12	0.3
2	1	A	244	medium positional	0.19	0.3
2	2	B	244	medium positional	0.23	0.3
2	3	C	244	medium positional	0.21	0.3
2	4	D	244	medium positional	0.15	0.3
1	1	A	421	loose positional	0.49	1.2
1	2	B	421	loose positional	0.53	1.2
1	3	C	421	loose positional	0.52	1.2
1	4	D	421	loose positional	0.49	1.2
2	1	A	490	loose positional	0.96	1.2
2	2	B	490	loose positional	1.19	1.2
2	3	C	490	loose positional	1.22	1.2
2	4	D	490	loose positional	1.06	1.2
1	1	A	257	medium thermal	0.96	2.5
1	2	B	257	medium thermal	1.03	2.5
1	3	C	257	medium thermal	1.21	2.5
1	4	D	257	medium thermal	1.18	2.5
2	1	A	244	medium thermal	1.08	2.5
2	2	B	244	medium thermal	1.28	2.5
2	3	C	244	medium thermal	1.27	2.5
2	4	D	244	medium thermal	1.13	2.5
1	1	A	421	loose thermal	1.67	5
1	2	B	421	loose thermal	1.48	5
1	3	C	421	loose thermal	1.66	5
1	4	D	421	loose thermal	1.44	5
2	1	A	490	loose thermal	2.06	5
2	2	B	490	loose thermal	3.11	5
2	3	C	490	loose thermal	2.5	5
2	4	D	490	loose thermal	2.03	5

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.27	403	-
R_work	0.226	8138	-
obs	-	-	90.17 %

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	1.4104	-0.2334	-0.2266	1.3758	0.5514	1.7141	-0.0619	0.0937	-0.0417	0.033	-0.0234	0.1622	-0.0044	-0.0469	0.0853	-0.0875	0.0077	-0.0055	-0.1107	-0.0015	-0.0959	-9.725	-0.721	-12.265
2	1.7204	0.0163	0.4536	1.1338	0.2816	1.5075	-0.0212	-0.062	0.0794	0.1291	0.0451	-0.0319	-0.1316	0.0846	-0.0238	-0.1005	-0.0368	0.0005	-0.0162	-0.0277	-0.093	27.351	8.358	34.629
3	29.2491	-5.9154	0.3286	3.3629	0.6839	1.9382	0.2195	1.016	2.4761	-0.3747	-0.0952	-0.7152	0.0625	0.3487	-0.1243	-0.031	0.0821	0.0371	0.0926	0.036	0.1486	30.907	7.96	68.472
4	0.6448	0.118	0.4577	1.4226	-0.0886	1.2985	0.0469	0.0329	0.0253	0.0638	-0.0664	0.2098	-0.0193	-0.0868	0.0196	-0.1455	-0.0041	0.0305	-0.0712	0.0056	-0.0276	-7.772	2.649	21.237
5	1.2747	0.0463	0.3112	0.6239	0.149	1.3258	0.0462	0.0473	0.0318	-0.0527	-0.0049	-0.0134	-0.0017	0.1106	-0.0413	-0.1471	-0.003	0.0107	-0.1071	-0.0272	-0.1069	19.658	-1.776	2.789
6	0.7412	0.0679	0.0214	0.6429	0.2616	0.9161	-0.0077	-0.0109	0.0168	-0.0353	0.0307	-0.042	0.0117	0.0957	-0.023	-0.155	-0.0174	0.006	-0.1003	-0.0232	-0.1155	20.648	-3.244	5.401
7	1.2496	0.2185	1.151	0.7373	0.6952	4.3258	-0.0209	-0.2047	0.0065	0.1958	0.0004	0.0007	0.4211	-0.1938	0.0205	-0.0322	0.0106	0.0291	-0.086	0.0106	-0.0884	3.541	-5.358	52.795
8	1.1213	0.0536	1.1786	0.8339	0.5781	4.0014	0.0436	-0.1635	-0.0582	0.1627	-0.0043	-0.0069	0.5015	-0.1276	-0.0393	-0.0318	-0.0053	0.0273	-0.0956	0.0103	-0.0897	2.956	-6.821	50.277

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 166	1 - 166
2	X-RAY DIFFRACTION	1	A	G	1350	1
3	X-RAY DIFFRACTION	2	B	B	1 - 166	1 - 166
4	X-RAY DIFFRACTION	2	B	H	2350	1
5	X-RAY DIFFRACTION	3	C	C	1 - 166	1 - 166
6	X-RAY DIFFRACTION	3	C	I	3350	1
7	X-RAY DIFFRACTION	4	D	D	1 - 166	1 - 166
8	X-RAY DIFFRACTION	4	D	J	4350	1
9	X-RAY DIFFRACTION	5	A	A	167 - 279	167 - 279
10	X-RAY DIFFRACTION	6	B	B	167 - 279	167 - 279
11	X-RAY DIFFRACTION	7	C	C	167 - 278	167 - 278
12	X-RAY DIFFRACTION	8	D	D	167 - 279	167 - 279

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