PDB-8sbv: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogen...

ID or keywords:

Entry

Database: PDB / ID: 8sbv

Title

Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (ADP bound)

Components

2,3-dihydroxybenzoate-2,3-dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE

Function / homology

Function and homology information

2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase / 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase activity / siderophore biosynthetic process / nucleotide binding
Similarity search - Function

Biological species

Klebsiella aerogenes KCTC 2190 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201700059C	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (ADP bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Apr 4, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sbv.cif.gz	179.4 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	8sbv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8sbv_validation.pdf.gz	786.6 KB	Display	wwPDB validaton report
Full document	8sbv_full_validation.pdf.gz	786.7 KB	Display
Data in XML	8sbv_validation.xml.gz	20.1 KB	Display
Data in CIF	8sbv_validation.cif.gz	29.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sb/8sbv ftp://data.pdbj.org/pub/pdb/validation_reports/sb/8sbv	HTTPS FTP

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Related structure data

Similar structure data	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	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: 2,3-dihydroxybenzoate-2,3-dehydrogenase

B: 2,3-dihydroxybenzoate-2,3-dehydrogenase

hetero molecules

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

1

A: 2,3-dihydroxybenzoate-2,3-dehydrogenase

hetero molecules

defined by author
Evidence: gel filtration
27.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 2,3-dihydroxybenzoate-2,3-dehydrogenase

hetero molecules

defined by author
28.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	67.520, 111.500, 58.109
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

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Protein , 1 types, 2 molecules AB

#1: Protein	2,3-dihydroxybenzoate-2,3-dehydrogenase Mass: 27572.984 Da / Num. of mol.: 2 / Mutation: A2N, A3G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria) Gene: EAE_13665 / Plasmid: KlaeA.01365.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FXS4

#1: Protein

2,3-dihydroxybenzoate-2,3-dehydrogenase

Mass: 27572.984 Da / Num. of mol.: 2 / Mutation: A2N, A3G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: EAE_13665 / Plasmid: KlaeA.01365.a.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FXS4

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Non-polymers , 5 types, 298 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 1.98 Å³/Da / Density % sol: 37.98 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.4 Details: 0.6 M ammonium sulfate, 0.1M sodium acetate pH 4.4. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. Plate: liu-S-078 well A7, Puck: PSL-0603, Cryo: 2.5 M lithium sulfate. 2mM NAD added prior to ...Details: 0.6 M ammonium sulfate, 0.1M sodium acetate pH 4.4. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. Plate: liu-S-078 well A7, Puck: PSL-0603, Cryo: 2.5 M lithium sulfate. 2mM NAD added prior to crystallization. However, ADP modeled in replace of NAD, as NAD appears to have been hydrolysed at acidic pH (4.4). The nicotimide side clearly not visible. One subunit of the protein binds ADP

Crystal

Density Matthews: 1.98 Å³/Da / Density % sol: 37.98 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 0.6 M ammonium sulfate, 0.1M sodium acetate pH 4.4. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. Plate: liu-S-078 well A7, Puck: PSL-0603, Cryo: 2.5 M lithium sulfate. 2mM NAD added prior to ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2022
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.55→111.5 Å / Num. obs: 64479 / % possible obs: 100 % / Redundancy: 13.2 % / CC_1/2: 1 / R_merge(I) obs: 0.057 / R_pim(I) all: 0.016 / R_rim(I) all: 0.059 / Χ²: 1.04 / Net I/σ(I): 21.3 / Num. measured all: 850931
Reflection shell	Resolution: 1.55→1.59 Å / % possible obs: 100 % / Redundancy: 12.7 % / R_merge(I) obs: 1.565 / Num. measured all: 60272 / Num. unique obs: 4730 / CC_1/2: 0.664 / R_pim(I) all: 0.454 / R_rim(I) all: 1.631 / Χ²: 1.06 / Net I/σ(I) obs: 1.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_4918: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→58.11 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.184	3196	4.97 %
R_work	0.162	-	-
obs	0.1631	64304	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.55→58.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3131	0	48	291	3470

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3277
X-RAY DIFFRACTION	f_angle_d	0.942	4465
X-RAY DIFFRACTION	f_dihedral_angle_d	13.778	1130
X-RAY DIFFRACTION	f_chiral_restr	0.056	521
X-RAY DIFFRACTION	f_plane_restr	0.008	584

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 (%)
1.55-1.57	0.2856	138	0.263	2647	X-RAY DIFFRACTION	100
1.57-1.6	0.2186	124	0.2462	2611	X-RAY DIFFRACTION	100
1.6-1.62	0.2376	137	0.2297	2637	X-RAY DIFFRACTION	100
1.62-1.65	0.2051	133	0.2117	2634	X-RAY DIFFRACTION	100
1.65-1.68	0.2245	142	0.199	2627	X-RAY DIFFRACTION	100
1.68-1.71	0.2259	124	0.1937	2658	X-RAY DIFFRACTION	100
1.71-1.75	0.2219	150	0.1782	2599	X-RAY DIFFRACTION	100
1.75-1.79	0.2023	127	0.1774	2628	X-RAY DIFFRACTION	100
1.79-1.83	0.1874	137	0.1731	2649	X-RAY DIFFRACTION	100
1.83-1.87	0.1945	115	0.1658	2668	X-RAY DIFFRACTION	100
1.87-1.93	0.1885	146	0.1904	2574	X-RAY DIFFRACTION	98
1.93-1.98	0.1757	138	0.1465	2645	X-RAY DIFFRACTION	100
1.98-2.05	0.1472	144	0.1411	2620	X-RAY DIFFRACTION	100
2.05-2.12	0.1673	142	0.1474	2649	X-RAY DIFFRACTION	100
2.12-2.2	0.1904	138	0.1432	2665	X-RAY DIFFRACTION	100
2.2-2.3	0.1962	140	0.1627	2616	X-RAY DIFFRACTION	99
2.3-2.43	0.1696	148	0.1455	2674	X-RAY DIFFRACTION	100
2.43-2.58	0.1686	142	0.1453	2642	X-RAY DIFFRACTION	100
2.58-2.78	0.1771	146	0.1564	2694	X-RAY DIFFRACTION	100
2.78-3.06	0.2208	141	0.1675	2688	X-RAY DIFFRACTION	100
3.06-3.5	0.1855	143	0.1583	2708	X-RAY DIFFRACTION	100
3.5-4.41	0.16	146	0.1382	2725	X-RAY DIFFRACTION	100
4.41-58.11	0.1805	155	0.1768	2850	X-RAY DIFFRACTION	99

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	1.044	0.6126	0.3601	0.6997	0.0702	1.0816	0.0372	0.0754	-0.129	-0.0922	-0.0022	0.1664	0.1248	-0.2236	0.0001	0.2607	-0.0184	0.0097	0.2273	0.0174	0.2627	12.5035	-24.704	15.6221
2	0.2634	-0.2352	0.151	1.2584	-0.4996	0.9908	0.0026	-0.0306	-0.0319	-0.0141	0.0783	0.1447	0.1105	-0.1153	-0	0.1848	-0.0181	-0.008	0.217	0.0254	0.1983	16.6677	-10.2498	16.7196
3	0.735	0.3801	-0.2175	0.3649	0.0038	0.1416	-0.0005	0.1239	-0.1423	-0.0755	-0.0066	-0.1975	0.1917	0.095	-0	0.2388	0.0186	0.0051	0.2386	0.003	0.2376	30.094	-16.0832	11.7568
4	0.5296	0.0682	-0.0372	0.1662	0.297	0.6148	-0.0581	-0.0993	0.0926	0.1165	-0.1092	-0.0584	-0.3446	-0.264	-0.0616	0.2647	0.0322	-0.0046	0.1719	0.0141	0.235	17.447	25.6318	11.1635
5	0.0058	-0.0102	0.0184	0.0152	-0.0286	0.0521	-0.0107	-0.2608	0.2904	0.0055	0.0221	-0.0952	-0.0858	0.1357	0	0.28	0.0172	0.0287	0.2444	-0.0368	0.2547	17.942	26.2179	18.4518
6	1.0995	0.1253	-0.2562	0.4014	-0.0896	0.4548	0.1951	-0.2353	0.1235	0.1133	-0.2188	0.3335	-0.1945	-0.4014	-0.0046	0.3092	0.0445	-0.0063	0.3094	-0.0078	0.3121	6.0764	21.447	12.2104
7	0.3941	-0.1774	-0.0986	0.4402	0.3359	0.4767	0.0602	-0.0382	0.0413	0.2246	0.1226	0.3426	-0.185	-0.1931	0.0001	0.2089	0.0206	0.0243	0.252	0.0188	0.2314	11.8147	6.4965	19.1098
8	0.2789	0.0347	-0.2038	0.9466	0.1638	0.2379	0.0153	0.0018	0.0709	-0.0783	0.0062	0.0161	-0.0265	-0.0082	-0	0.1916	0.0077	0.0057	0.2171	0.0154	0.2055	18.7515	8.8462	9.6256
9	0.1246	0.0967	-0.0079	0.1577	-0.0795	0.0642	-0.0602	-0.0511	0.0926	0.0852	-0.1175	-0.1137	-0.1986	0.0386	-0	0.2444	0.0108	-0.0219	0.2211	-0.0064	0.2099	24.9853	14.9296	14.9606
10	0.3778	-0.2815	0.0594	0.3224	0.1534	0.3462	0.0427	-0.0889	0.1728	0.0253	-0.0427	-0.1686	-0.1477	0.1012	-0	0.224	-0.0112	0.0011	0.2262	-0.0111	0.2386	29.3885	16.4	15.4613

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 70 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 71 through 168 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 169 through 251 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 4 through 18 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 19 through 30 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 31 through 72 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 73 through 107 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 108 through 168 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 169 through 217 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 218 through 251 )

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