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- PDB-7swk: NAD/NADP-dependent betaine aldehyde dehydrogenase from Klebsiella... -

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Basic information

Entry
Database: PDB / ID: 7swk
TitleNAD/NADP-dependent betaine aldehyde dehydrogenase from Klebsiella pneumoniae subsp. pneumoniae
ComponentsBetaine aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / betB / Betaine / aldehyde / dehydrogenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / metal ion binding
Similarity search - Function
Betaine aldehyde dehydrogenase / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
ACETATE ION / Betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: NAD/NADP-dependent betaine aldehyde dehydrogenase from Klebsiella pneumoniae subsp. pneumoniae
Authors: DeBouver, N.D. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Betaine aldehyde dehydrogenase
B: Betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5958
Polymers108,0042
Non-polymers5916
Water19,2761070
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-57 kcal/mol
Surface area32240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.350, 165.690, 167.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Betaine aldehyde dehydrogenase / BADH


Mass: 54002.027 Da / Num. of mol.: 2 / Fragment: BupsE.01646.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain HS11286) (bacteria)
Strain: HS11286 / Gene: betB, KPHS_14160 / Plasmid: BupsE.01646.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H3GTN1, betaine-aldehyde dehydrogenase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1070 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: KlpnC.00252.a.B1.PW38989 [Barcode: 321954b11, PuckID: yis2-2, Cryo: Direct, BEAMLINE: APS21idf, Collected date: 07292021, Concentration: 10 mg/mL] 100 mM Sodium citrate tribasic / ...Details: KlpnC.00252.a.B1.PW38989 [Barcode: 321954b11, PuckID: yis2-2, Cryo: Direct, BEAMLINE: APS21idf, Collected date: 07292021, Concentration: 10 mg/mL] 100 mM Sodium citrate tribasic / Hydrochloric Acid pH 5.6, 30.0% (v/v) MPD, 200 mM Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 18, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→40.22 Å / Num. obs: 110953 / % possible obs: 99.7 % / Redundancy: 6.073 % / Biso Wilson estimate: 20.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.073 / Χ2: 0.921 / Net I/σ(I): 17.27 / Num. measured all: 673798
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.856.2080.5663.2350583815381480.9340.61999.9
1.85-1.96.2030.4653.9149263794979420.9480.50899.9
1.9-1.956.1970.3724.8247917773877320.9670.40799.9
1.95-2.016.2030.2995.9946512750974980.9760.32799.9
2.01-2.086.1740.2327.6745091731373030.9850.25399.9
2.08-2.156.1820.1849.5843452704070290.9880.20199.8
2.15-2.236.1410.1610.9441866682868170.9910.17599.8
2.23-2.326.130.13212.9640173656265540.9930.14599.9
2.32-2.436.070.11114.9738035628262660.9940.12299.7
2.43-2.556.0060.09517.1436291605360420.9960.10499.8
2.55-2.685.9750.0819.7534194573857230.9970.08899.7
2.68-2.855.9460.06822.1232273544754280.9970.07599.7
2.85-3.045.8830.05626.3329979511150960.9980.06299.7
3.04-3.295.7840.04631.6827615478547740.9980.0599.8
3.29-3.65.7950.03936.9225482442243970.9990.04399.4
3.6-4.025.9220.03341.3323540399539750.9990.03799.5
4.02-4.655.9990.02944.8521223356135380.9990.03299.4
4.65-5.696.1110.02943.3518358302430040.9990.03299.3
5.69-8.056.0920.02742.7714303236923480.9990.0399.1
8.05-40.225.7120.02446.67648138113390.9990.02797

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20rc1_4392refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CBB

4cbb


Resolution: 1.8→40.22 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1745 2082 1.88 %
Rwork0.1463 108782 -
obs0.1468 110864 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.53 Å2 / Biso mean: 23.0088 Å2 / Biso min: 8.81 Å2
Refinement stepCycle: final / Resolution: 1.8→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7351 0 40 1093 8484
Biso mean--34.23 32.12 -
Num. residues----975
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.22821230.2171937316100
1.84-1.890.29111260.200571927318100
1.89-1.940.24391410.181871827323100
1.94-20.22051420.181272137355100
2-2.060.2051370.170472177354100
2.06-2.130.22151460.15672147360100
2.13-2.220.19031050.152472437348100
2.22-2.320.19341480.150772177365100
2.32-2.440.18581540.150372227376100
2.44-2.60.18681450.151972467391100
2.6-2.80.16711450.153172237368100
2.8-3.080.17171520.14972897441100
3.08-3.520.15041270.133972927419100
3.52-4.440.13511410.11647340748199
4.44-40.220.15371500.13377499764999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.7373-0.05080.4631.1197-0.36231.9187-0.0655-0.07270.07520.11370.0296-0.1209-0.1320.24040.03470.08360.0026-0.00810.205-0.03130.1506-16.86992.0455-19.8897
20.2915-0.02330.0940.3817-0.01340.6111-0.0324-0.0384-0.03640.07370.0485-0.04610.04690.1016-0.01240.11510.03110.0010.1554-0.01130.1272-27.8209-7.0125-23.7693
31.2250.14220.28431.12550.02130.8109-0.0784-0.1792-0.19980.31320.153-0.30090.20430.0935-0.05440.35540.1329-0.04260.20630.00880.2455-25.3011-33.542-15.7987
40.3508-0.19830.09680.9898-0.13010.5477-0.0563-0.0649-0.06340.15520.08310.02220.0976-0.01-0.02650.13640.02460.01630.12660.00910.1057-40.2313-17.6168-24.7661
50.3929-0.0753-0.64481.42520.61311.45380.0296-0.02250.00030.0463-0.05750.19560.0394-0.34370.04370.14030.03060.02550.29940.01480.1926-73.02630.6932-8.9438
60.6481-0.1178-0.63171.34050.47571.9326-0.0416-0.0008-0.1393-0.01080.0020.06420.2914-0.15710.04110.1133-0.02990.02530.17680.01540.1649-65.0661-9.6724-27.1324
70.2567-0.0115-0.11050.32610.01830.579-0.0208-0.03290.05740.11090.04290.0213-0.0384-0.0956-0.01760.14080.02940.01150.15530.00130.1384-57.63194.0552-23.0281
80.84620.011-0.19810.97060.30431.034-0.1143-0.18750.17480.33390.13940.2909-0.2643-0.1318-0.03010.41960.13380.0730.2164-0.0120.2651-59.83830.4267-14.9047
90.342-0.0811-0.06040.78560.03310.4659-0.0497-0.07010.08750.1990.0713-0.0096-0.10.0177-0.01810.16260.025-0.00680.131-0.02060.1132-45.342314.5915-24.7137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 81 )A4 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 290 )A82 - 290
3X-RAY DIFFRACTION3chain 'A' and (resid 291 through 363 )A291 - 363
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 490 )A364 - 490
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 42 )B3 - 42
6X-RAY DIFFRACTION6chain 'B' and (resid 43 through 81 )B43 - 81
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 290 )B82 - 290
8X-RAY DIFFRACTION8chain 'B' and (resid 291 through 363 )B291 - 363
9X-RAY DIFFRACTION9chain 'B' and (resid 364 through 490 )B364 - 490

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