PDB-8skf: Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from K...

ID or keywords:

Entry

Database: PDB / ID: 8skf

Title

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (Lattice Translocation Disorder)

Components

Betaine aldehyde dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / BetB / lattice translocation disorder

Function / homology

Function and homology information

betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / glycine betaine biosynthetic process from choline / metal ion binding
Similarity search - Function

Biological species

Klebsiella aerogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 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 Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (Lattice Translocation Disorder)
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A.

History

Deposition	Apr 19, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 26, 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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PDBx/mmCIF format	8skf.cif.gz	407.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8skf.ent.gz	330.9 KB	Display	PDB format
PDBx/mmJSON format	8skf.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/sk/8skf ftp://data.pdbj.org/pub/pdb/validation_reports/sk/8skf	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	#127 - Jul 2010 Crystallins similarity (7) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (7)

Deposited unit

A: Betaine aldehyde dehydrogenase

B: Betaine aldehyde dehydrogenase

hetero molecules

111 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)	85.822, 184.823, 163.066
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Betaine aldehyde dehydrogenase Mass: 54062.281 Da / Num. of mol.: 2 / Mutation: V62A, Q485P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: betB_3 / Plasmid: KlaeA.00020.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A447LC14

#1: Protein

Betaine aldehyde dehydrogenase

Mass: 54062.281 Da / Num. of mol.: 2 / Mutation: V62A, Q485P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Klebsiella aerogenes (bacteria) / Gene: betB_3 / Plasmid: KlaeA.00020.b.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A447LC14

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Non-polymers , 5 types, 824 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 813 / 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: 2.99 Å³/Da / Density % sol: 58.87 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: JCSG+ C4: 10% (w/v) PEG 6K, 0.10 M HEPES pH 7.0, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. Plate: 13125, well C4 drop 2. Puck: PSL-0714, Cryo: 20% PEG200 + 80% crystallant. 2mM NAD added prior ...Details: JCSG+ C4: 10% (w/v) PEG 6K, 0.10 M HEPES pH 7.0, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. Plate: 13125, well C4 drop 2. Puck: PSL-0714, Cryo: 20% PEG200 + 80% crystallant. 2mM NAD added prior to crystallization. The intensities were corrected for lattice translocation disorder which orginally caused high Rfactors (~25% and 29% for R and Rfree) and residual positive electron density throughout the polypeptide chains. The correction was based on major non-origin Patterson peaks, 1) (0.500, 0.027, 0.500) and its inverse (0.500, -0.027, 0.500) and 2) (0.000, 0.054, 0.000) PH range: '

Crystal

Density Matthews: 2.99 Å³/Da / Density % sol: 58.87 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: JCSG+ C4: 10% (w/v) PEG 6K, 0.10 M HEPES pH 7.0, KlaeA.00020.b.B1.PW39167 at 17 mg/mL. Plate: 13125, well C4 drop 2. Puck: PSL-0714, Cryo: 20% PEG200 + 80% crystallant. 2mM NAD added prior ...
PH range: '

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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: 1.8→163.07 Å / Num. obs: 119740 / % possible obs: 100 % / Redundancy: 13.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.155 / R_pim(I) all: 0.043 / R_rim(I) all: 0.161 / Χ²: 1.01 / Net I/σ(I): 10.5 / Num. measured all: 1639041
Reflection shell	Resolution: 1.8→1.85 Å / % possible obs: 99.9 % / Redundancy: 13.5 % / R_merge(I) obs: 1.439 / Num. measured all: 118437 / Num. unique obs: 8785 / CC_1/2: 0.886 / R_pim(I) all: 0.404 / R_rim(I) all: 1.495 / Χ²: 1 / Net I/σ(I) obs: 1.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_4932: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→81.53 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.63 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2074	5962	4.99 %
R_work	0.1741	-	-
obs	0.1758	119370	99.69 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→81.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7492	0	152	813	8457

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7992
X-RAY DIFFRACTION	f_angle_d	0.99	10852
X-RAY DIFFRACTION	f_dihedral_angle_d	14.458	2926
X-RAY DIFFRACTION	f_chiral_restr	0.056	1200
X-RAY DIFFRACTION	f_plane_restr	0.01	1417

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 (%)
1.8-1.82	0.3471	189	0.2865	3741	X-RAY DIFFRACTION	99
1.82-1.84	0.3035	211	0.2719	3708	X-RAY DIFFRACTION	99
1.84-1.86	0.2868	194	0.2567	3767	X-RAY DIFFRACTION	100
1.86-1.89	0.2975	193	0.2569	3726	X-RAY DIFFRACTION	100
1.89-1.91	0.3046	208	0.2569	3707	X-RAY DIFFRACTION	100
1.91-1.94	0.2961	163	0.2499	3791	X-RAY DIFFRACTION	99
1.94-1.97	0.2795	206	0.2366	3727	X-RAY DIFFRACTION	99
1.97-2	0.2316	186	0.2331	3773	X-RAY DIFFRACTION	100
2-2.03	0.2768	183	0.2308	3741	X-RAY DIFFRACTION	100
2.03-2.06	0.2639	205	0.2091	3745	X-RAY DIFFRACTION	100
2.06-2.1	0.2422	236	0.1937	3735	X-RAY DIFFRACTION	100
2.1-2.13	0.228	179	0.1832	3777	X-RAY DIFFRACTION	100
2.13-2.18	0.2361	182	0.1818	3792	X-RAY DIFFRACTION	100
2.18-2.22	0.2056	197	0.1773	3738	X-RAY DIFFRACTION	100
2.22-2.27	0.2064	218	0.1758	3768	X-RAY DIFFRACTION	100
2.27-2.32	0.211	208	0.1636	3750	X-RAY DIFFRACTION	100
2.32-2.38	0.1948	197	0.1573	3762	X-RAY DIFFRACTION	100
2.38-2.44	0.1959	206	0.1542	3780	X-RAY DIFFRACTION	100
2.44-2.51	0.1862	192	0.16	3778	X-RAY DIFFRACTION	100
2.51-2.6	0.1971	210	0.1536	3788	X-RAY DIFFRACTION	100
2.6-2.69	0.1821	219	0.1574	3759	X-RAY DIFFRACTION	100
2.69-2.8	0.2172	175	0.1584	3783	X-RAY DIFFRACTION	100
2.8-2.92	0.1967	197	0.1602	3817	X-RAY DIFFRACTION	100
2.92-3.08	0.1849	210	0.1696	3790	X-RAY DIFFRACTION	100
3.08-3.27	0.1918	188	0.1785	3795	X-RAY DIFFRACTION	100
3.27-3.52	0.2167	226	0.1705	3809	X-RAY DIFFRACTION	100
3.52-3.88	0.2017	181	0.1549	3830	X-RAY DIFFRACTION	100
3.88-4.44	0.1594	214	0.1313	3841	X-RAY DIFFRACTION	100
4.44-5.59	0.1546	196	0.1297	3889	X-RAY DIFFRACTION	100
5.59-81.53	0.1798	193	0.1751	4001	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	1.4577	0.4491	0.0855	0.6479	-0.2698	1.1359	-0.0401	-0.0557	0.0284	0.2407	0.039	-0.0237	-0.0553	0.1463	-0.0179	0.1455	0.0293	0.0201	0.2195	0.0008	0.1404	31.8913	51.5631	-6.9346
2	3.2146	0.2706	0.2735	1.7911	0.3243	1.0859	0.0277	-0.0157	-0.5304	-0.003	-0.0455	0.1247	0.1588	-0.0005	0.0699	0.1758	0.005	0.0622	0.1379	0.0379	0.1421	15.4412	35.7451	-19.1084
3	0.3757	0.2312	0.1588	0.5288	0.2673	0.5313	-0.0002	-0.0211	-0.0029	0.006	-0.0003	-0.0573	-0.0102	0.062	0.0077	0.181	0.0077	0.0672	0.182	0.0086	0.1767	17.5293	44.5054	-23.0701
4	1.157	-1.1527	0.1913	2.5207	0.0281	0.2488	0.0232	0.1238	-0.0528	-0.0328	-0.0668	0.0087	0.0238	0.0986	0.0431	0.2167	-0.024	0.0576	0.2074	-0.0044	0.1964	22.3215	60.9535	-32.3773
5	0.9496	-0.2295	0.0692	1.9234	-0.9096	1.9168	0.0223	-0.0516	0.1261	0.3056	-0.0296	-0.1609	-0.2009	0.1731	0.0159	0.2201	-0.0628	0.0157	0.1421	-0.0385	0.2122	26.2711	76.0474	-22.7792
6	0.9184	0.3484	0.3959	0.9753	0.188	0.481	-0.0066	0.0711	0.0339	0.0172	0.0022	-0.0669	-0.0482	0.0788	0.0151	0.1912	-0.0193	0.071	0.1622	0.0033	0.1725	19.197	68.5161	-36.465
7	1.0771	-0.3122	-0.5751	0.264	0.1417	1.0121	-0.0114	0.0796	-0.0492	-0.0894	-0.0236	-0.0672	0.0559	-0.0363	0.0644	0.1901	0.0067	0.0566	0.1858	0.0277	0.1624	8.9769	28.4558	-44.8832
8	0.8708	-0.2125	-0.3475	4.1551	-0.154	0.1515	-0.0645	0.3103	-0.0031	-0.6135	0.0381	-0.2735	-0.0147	0.0104	-0.0059	0.219	-0.018	0.0833	0.2999	0.023	0.1766	32.42	40.4867	-72.0432
9	0.1345	-0.0636	-0.0315	0.5671	0.3704	0.6307	-0.005	0.0633	0.0573	-0.0406	-0.0126	-0.0509	0.0068	0.0075	0.0152	0.1621	-0.0001	0.0611	0.1767	0.0207	0.1817	14.7131	44.4539	-59.7354
10	0.4229	0.1747	-0.1535	1.0247	-0.3331	0.3321	-0.0259	0.0318	-0.0359	-0.01	-0.0026	-0.0818	0.0772	0.0894	0.023	0.1807	0.024	0.068	0.1939	-0.015	0.1893	25.0574	23.4506	-55.1073
11	0.1518	-0.1371	-0.0216	0.6723	0.1724	0.2995	-0.0093	-0.0335	-0.0342	0.0069	0.0143	-0.0639	0.0513	0.0567	-0.014	0.1551	0.0139	0.0735	0.1733	0.0073	0.1755	17.1906	26.7384	-43.4297

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -6 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 81 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 82 through 230 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 231 through 290 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 291 through 363 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 364 through 465 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 466 through 490 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 42 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 43 through 195 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 196 through 363 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 364 through 490 )

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