PDB-4ywj: Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (...

ID or keywords:

Entry

Database: PDB / ID: 4ywj

Title

Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (HTPA reductase) from Pseudomonas aeruginosa

Components

4-hydroxy-tetrahydrodipicolinate reductase

Keywords

OXIDOREDUCTASE / SSGCID / Pseudomonas aeruginosa / 4-hydroxy-tetrahydrodipicolinate reductase / HTPA reductase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (HTPA reductase) from Pseudomonas aeruginosa
Authors: Abendroth, J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Mar 20, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 1, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ywj.cif.gz	225.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ywj.ent.gz	178.6 KB	Display	PDB format
PDBx/mmJSON format	4ywj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ywj_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4ywj_full_validation.pdf.gz	1 MB	Display
Data in XML	4ywj_validation.xml.gz	25.9 KB	Display
Data in CIF	4ywj_validation.cif.gz	36.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yw/4ywj ftp://data.pdbj.org/pub/pdb/validation_reports/yw/4ywj	HTTPS FTP

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Related structure data

Related structure data	1arzS S: Starting model for refinement
Similar structure data	6smy-d 1dih-1 1drw-1 4ae0-1 5i82-1 6wxx-2 3qy9-d 5mzu-d 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
Other databases	TargetTrack: SSGCID-PsaeA.00820.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#100 - Apr 2008 Adrenergic Receptors similarity (1) #193 - Jan 2016 Siderocalin similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1)

Deposited unit

A: 4-hydroxy-tetrahydrodipicolinate reductase

B: 4-hydroxy-tetrahydrodipicolinate reductase

hetero molecules

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

1

A: 4-hydroxy-tetrahydrodipicolinate reductase

B: 4-hydroxy-tetrahydrodipicolinate reductase

hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase

B: 4-hydroxy-tetrahydrodipicolinate reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	93.010, 101.500, 144.510
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-550- HOH
2	1	A-585- HOH
3	1	B-538- HOH
4	1	B-565- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	4-hydroxy-tetrahydrodipicolinate reductase / HTPA reductase Mass: 29392.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: dapB, PA4759 / Plasmid: PsaeA.00820.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P38103, 4-hydroxy-tetrahydrodipicolinate reductase

#1: Protein

4-hydroxy-tetrahydrodipicolinate reductase / HTPA reductase

Mass: 29392.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: dapB, PA4759 / Plasmid: PsaeA.00820.a.B1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P38103, 4-hydroxy-tetrahydrodipicolinate reductase

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Non-polymers , 5 types, 363 molecules

#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-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-BU1 / 1,4-BUTANEDIOL Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.91 Å³/Da / Density % sol: 58 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Morpheus D9: 20mM of each: 1,6-Hexanediol; 1-Butanol, 1,2-Propanediol (racemic); 2-Propanol; 1,4-Butanediol; 1,3-Propanediol; 100mM Tris Base / Bicine pH 8.5, 30% each PEG 550MME, PEG 20000; ...Details: Morpheus D9: 20mM of each: 1,6-Hexanediol; 1-Butanol, 1,2-Propanediol (racemic); 2-Propanol; 1,4-Butanediol; 1,3-Propanediol; 100mM Tris Base / Bicine pH 8.5, 30% each PEG 550MME, PEG 20000; PsaeA.00820.a.B1.PW37541 at 22.65 mg/ml; cryo: direct; tray 259740d90, puck hxm4-4

Crystal

Density Matthews: 2.91 Å³/Da / Density % sol: 58 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus D9: 20mM of each: 1,6-Hexanediol; 1-Butanol, 1,2-Propanediol (racemic); 2-Propanol; 1,4-Butanediol; 1,3-Propanediol; 100mM Tris Base / Bicine pH 8.5, 30% each PEG 550MME, PEG 20000; ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 25, 2014

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: 1.8→50 Å / Num. obs: 63326 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5 % / B_iso Wilson estimate: 24.1 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.048 / R_rim(I) all: 0.053 / Χ²: 1.035 / Net I/σ(I): 18.11 / Num. measured all: 316725

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.8-1.85	5.2	0.837	0.517	2.9	24010	4656	4654	0.578	100
1.85-1.9		0.914	0.419	3.55	23598	4569	4562	0.468	99.8
1.9-1.95		0.949	0.298	5.04	22630	4408	4401	0.333	99.8
1.95-2.01		0.972	0.226	6.55	21785	4284	4278	0.252	99.9
2.01-2.08		0.975	0.189	7.92	21287	4189	4182	0.21	99.8
2.08-2.15		0.982	0.158	9.3	20353	4044	4040	0.176	99.9
2.15-2.23		0.988	0.123	11.64	19435	3885	3879	0.137	99.8
2.23-2.32		0.991	0.101	13.95	18666	3771	3755	0.113	99.6
2.32-2.43		0.993	0.088	15.93	17719	3584	3572	0.098	99.7
2.43-2.55		0.996	0.072	18.77	16764	3437	3426	0.08	99.7
2.55-2.68		0.996	0.064	20.56	16064	3310	3288	0.072	99.3
2.68-2.85		0.997	0.053	24.78	14907	3118	3086	0.059	99
2.85-3.04		0.998	0.044	28.84	14015	2925	2900	0.049	99.1
3.04-3.29		0.999	0.038	32.82	13096	2754	2721	0.043	98.8
3.29-3.6		0.999	0.032	38.65	12149	2520	2491	0.036	98.8
3.6-4.02		0.999	0.028	42.54	11258	2297	2273	0.031	99
4.02-4.65		0.999	0.024	46.05	10234	2055	2030	0.026	98.8
4.65-5.69		1	0.022	45.97	8743	1743	1717	0.024	98.5
5.69-8.05		1	0.02	45.74	6665	1359	1326	0.023	97.6
8.05-50		0.999	0.018	46.34	3347	808	745	0.02	92.2

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Processing

Software

Name	Version	Classification
XDS		data reduction
PHASER		phasing
ARP		model building
Coot		model building
PHENIX	dev_1980	refinement
PDB_EXTRACT		data extraction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ARZ

1arz

Resolution: 1.8→34.287 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2006	3153	5.01 %	Random selection
R_work	0.1677	59774	-	-
obs	0.1694	62927	99.1 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 108.18 Å² / B_iso mean: 36.7854 Å² / B_iso min: 10.95 Å²

Refinement step

Cycle: final / Resolution: 1.8→34.287 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3872	0	121	356	4349
B_iso mean	-	-	40.04	39.06	-
Num. residues	-	-	-	-	536

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4111
X-RAY DIFFRACTION	f_angle_d	0.991	5580
X-RAY DIFFRACTION	f_chiral_restr	0.048	655
X-RAY DIFFRACTION	f_plane_restr	0.004	729
X-RAY DIFFRACTION	f_dihedral_angle_d	15.896	1466

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 (%)
1.8-1.8269	0.3228	126	0.2781	2425	X-RAY DIFFRACTION	94
1.8269-1.8554	0.2773	155	0.2639	2586	X-RAY DIFFRACTION	100
1.8554-1.8858	0.2806	131	0.2435	2571	X-RAY DIFFRACTION	100
1.8858-1.9183	0.2804	134	0.2174	2619	X-RAY DIFFRACTION	100
1.9183-1.9532	0.2468	129	0.204	2591	X-RAY DIFFRACTION	100
1.9532-1.9908	0.219	128	0.1972	2566	X-RAY DIFFRACTION	100
1.9908-2.0314	0.2138	158	0.1868	2614	X-RAY DIFFRACTION	100
2.0314-2.0756	0.2518	138	0.1913	2566	X-RAY DIFFRACTION	100
2.0756-2.1239	0.1945	130	0.19	2609	X-RAY DIFFRACTION	100
2.1239-2.177	0.2	140	0.1876	2578	X-RAY DIFFRACTION	100
2.177-2.2358	0.2318	139	0.1875	2599	X-RAY DIFFRACTION	100
2.2358-2.3016	0.2612	142	0.1793	2610	X-RAY DIFFRACTION	100
2.3016-2.3759	0.2073	134	0.1788	2615	X-RAY DIFFRACTION	100
2.3759-2.4608	0.2174	146	0.1655	2602	X-RAY DIFFRACTION	100
2.4608-2.5592	0.1975	129	0.1633	2617	X-RAY DIFFRACTION	100
2.5592-2.6757	0.2128	133	0.1745	2589	X-RAY DIFFRACTION	99
2.6757-2.8167	0.2075	147	0.1734	2581	X-RAY DIFFRACTION	99
2.8167-2.9931	0.2221	133	0.1728	2631	X-RAY DIFFRACTION	99
2.9931-3.224	0.1971	136	0.1732	2582	X-RAY DIFFRACTION	99
3.224-3.5481	0.1832	140	0.159	2625	X-RAY DIFFRACTION	99
3.5481-4.0609	0.1697	131	0.1418	2653	X-RAY DIFFRACTION	99
4.0609-5.1135	0.1533	135	0.1285	2642	X-RAY DIFFRACTION	99
5.1135-50	0.1819	139	0.1539	2703	X-RAY DIFFRACTION	97

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	4.2504	0.0212	-0.055	3.9624	-0.9154	5.5622	-0.0037	-0.1989	0.6663	0.2577	0.0037	-0.4499	-0.1231	0.791	0.015	0.2026	0.0561	-0.023	0.3963	-0.0434	0.4296	48.0383	43.7255	14.5955
2	1.1899	0.2519	-0.2716	3.1096	0.1042	3.4887	-0.0791	-0.0953	0.759	-0.0446	-0.0628	-0.6955	-0.1703	1.0476	0.0444	0.2824	0.0303	0.0134	0.6359	-0.0624	0.6838	55.1064	44.2709	13.2717
3	2.6422	0.3829	1.666	0.7444	-1.0368	3.3974	-0.0443	-0.1657	0.3802	0.2123	-0.0174	-0.8687	-0.0606	1.1057	0.0213	0.3027	0.1211	-0.0496	0.6293	-0.0656	0.557	53.9042	40.0051	16.5465
4	1.7298	-0.5435	0.6072	1.4021	0.1929	1.7454	-0.1043	-0.4092	-0.2246	0.3176	0.1943	-0.4189	0.6293	0.4734	-0.0623	0.4468	0.367	-0.0669	0.4351	-0.0492	0.3633	48.3662	28.3366	17.5002
5	1.1412	-0.4481	0.2087	0.5357	0.1031	1.157	-0.1681	-0.1624	-0.2754	0.1504	0.1454	-0.1184	0.3707	0.1339	-0.052	0.2833	0.0755	0.0288	0.1391	0.0089	0.2457	28.3197	33.0051	10.1336
6	1.7112	0.7256	-0.2241	1.1762	-0.325	1.1671	-0.0614	-0.0826	-0.663	0.1177	-0.0129	-0.1058	0.5452	0.0209	-0.0338	0.3411	0.0221	0.0571	0.1355	0.019	0.3496	18.8794	28.0207	6.5204
7	1.3094	-0.0814	0.0359	0.7218	-0.0973	1.4218	-0.117	0.0518	-0.285	-0.0726	0.0804	-0.0476	0.2303	-0.1174	0.0417	0.1993	-0.0187	0.0284	0.1177	-0.0185	0.1819	16.2854	38.1943	-0.448
8	2.7259	-0.6853	0.1665	3.1008	-1.3199	3.472	-0.1643	-0.47	0.0744	0.2274	0.1929	0.0229	0.3433	0.2362	0.0035	0.2667	0.1388	-0.0062	0.2789	-0.0411	0.2087	36.2905	37.647	20.3712
9	3.388	-0.0482	1.4501	3.257	-0.0604	2.8184	-0.0465	0.4393	-0.1776	-0.183	0.3365	1.064	0.202	-0.7189	-0.1286	0.2612	0.0025	-0.0093	0.7356	0.0929	0.5413	-15.2839	44.5773	12.7038
10	3.5638	1.0635	2.8839	1.3027	0.8908	2.4766	0.102	-0.0412	0.0046	0.0946	0.0648	1.0719	0.1805	-0.9528	-0.2387	0.3734	0.0101	0.1041	0.7354	0.0721	0.66	-18.0117	44.6763	17.6485
11	1.0789	-0.0111	0.1485	1.4066	-0.1098	1.4967	-0.143	-0.3605	0.1102	0.3071	0.117	0.0825	-0.0804	-0.2463	-0.0472	0.2257	0.0926	0.0239	0.2486	-0.0448	0.1285	9.861	54.3948	18.9743
12	2.0323	0.0706	-0.6137	2.377	-0.7871	5.4377	-0.2027	-0.4054	-0.213	0.3728	0.1692	0.1649	0.2808	-0.167	0.0733	0.2701	0.0239	0.0796	0.4006	0.0487	0.2319	-0.3495	41.5517	21.6489

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 22 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 49 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 78 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 79 through 104 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 105 through 165 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 166 through 186 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 187 through 236 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 237 through 268 )	A
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 50 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 51 through 78 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 79 through 236 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 237 through 268 )	B

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Components

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 363 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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