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- PDB-6wsa: Crystal structure of a betaine aldehyde dehydrogenase from Burkho... -

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Basic information

Entry
Database: PDB / ID: 6wsa
TitleCrystal structure of a betaine aldehyde dehydrogenase from Burkholderia pseudomallei without cofactor
ComponentsNAD/NADP-dependent betaine aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / National Institute of Allergy and Infectious Disease / NIAID / melioidosis / glycine metabolism / serine metabolism / threonine metabolism / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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
Betaine aldehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 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 ...Betaine aldehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SUCCINIC ACID / Betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structure of betaine aldehyde dehydrogenase from Burkholderia pseudomallei.
Authors: Beard, D.K. / Subramanian, S. / Abendroth, J. / Dranow, D.M. / Edwards, T.E. / Myler, P.J. / Asojo, O.A.
History
DepositionApr 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 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: NAD/NADP-dependent betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,08116
Polymers53,1331
Non-polymers94815
Water9,026501
1
A: NAD/NADP-dependent betaine aldehyde dehydrogenase
hetero molecules

A: NAD/NADP-dependent betaine aldehyde dehydrogenase
hetero molecules

A: NAD/NADP-dependent betaine aldehyde dehydrogenase
hetero molecules

A: NAD/NADP-dependent betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,32464
Polymers212,5324
Non-polymers3,79260
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_664-y+1,-x+1,-z-1/31
Buried area30920 Å2
ΔGint-3 kcal/mol
Surface area57720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.860, 107.860, 233.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-899-

HOH

21A-921-

HOH

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Components

#1: Protein NAD/NADP-dependent betaine aldehyde dehydrogenase / BADH


Mass: 53132.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria)
Strain: 1710b / Gene: betB, BURPS1710b_A0376 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JLL8, betaine-aldehyde dehydrogenase
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: BupsA.00020.b.AE1.PS38619 at 34.72 mg/mL against JCSG+ screen condition F7: 0.8 M succinate pH 7.0 supplemented with 20% ethylene glycol as cryo-protectant, unique puck ID gfm8-1, crystal tracking ID 314025f7

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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 MX300HE / Detector: CCD / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→49.51 Å / Num. obs: 51154 / % possible obs: 99.9 % / Redundancy: 7.085 % / Biso Wilson estimate: 32.748 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.101 / Χ2: 1.056 / Net I/σ(I): 12.86 / Num. measured all: 362438 / Scaling rejects: 9
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
2.05-2.17.280.5083.526952370437020.9480.54899.9
2.1-2.167.3410.4234.0426656363136310.9570.455100
2.16-2.227.3220.3494.9225709351235110.9670.375100
2.22-2.297.1970.315.6924641342534240.9750.334100
2.29-2.377.3140.2436.7324106329632960.9860.261100
2.37-2.457.2960.2087.9823654324232420.9870.224100
2.45-2.547.2830.1849.0422622310631060.9880.198100
2.54-2.657.2680.15510.7221848300630060.9910.167100
2.65-2.767.180.14112.0320809289828980.9920.152100
2.76-2.97.1690.12313.8519664274327430.9940.132100
2.9-3.067.1230.10315.8718884265126510.9950.111100
3.06-3.246.9840.08818.1417524250925090.9960.095100
3.24-3.476.8390.07720.3916201236923690.9960.083100
3.47-3.746.7340.07122.4414922221622160.9970.076100
3.74-4.16.6410.06324.1613528203720370.9970.068100
4.1-4.586.6590.05525.9412425186718660.9980.05999.9
4.58-5.296.6930.05226.0611151167016660.9980.05699.8
5.29-6.486.70.04925.159695144814470.9980.05399.9
6.48-9.176.5020.03827.037451114711460.9990.04199.9
9.17-49.515.8080.03426.3239967056880.9980.03797.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.17.1.3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wox

2wox


Resolution: 2.05→49.51 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.19
RfactorNum. reflection% reflection
Rfree0.1729 2932 5.96 %
Rwork0.1404 --
obs0.1424 49171 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.28 Å2 / Biso mean: 34.255 Å2 / Biso min: 17.2 Å2
Refinement stepCycle: final / Resolution: 2.05→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 61 501 4228
Biso mean--58.43 42.54 -
Num. residues----489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.080.25211090.22031957206687
2.08-2.120.23911250.19232047217290
2.12-2.160.20841290.17542036216591
2.16-2.20.2321240.16422080220492
2.2-2.240.17631240.16632078220292
2.24-2.290.22761560.16992046220292
2.29-2.350.21291310.14612118224994
2.35-2.410.19591500.1432124227496
2.41-2.470.191350.14332199233497
2.47-2.540.18291280.14522196232497
2.54-2.630.17271410.14652236237798
2.63-2.720.19511270.15132228235598
2.72-2.830.18741420.15282244238698
2.83-2.960.20951500.15732240239099
2.96-3.110.18061420.14842267240999
3.11-3.310.21081470.15012271241899
3.31-3.560.15951550.137823052460100
3.56-3.920.15841470.122523142461100
3.92-4.490.12331560.106823342490100
4.49-5.650.12491550.113623742529100
5.65-49.510.17241590.1442545270499
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)
11.33410.9873-0.66572.0275-0.56051.2980.1176-0.21830.12560.1668-0.02980.2853-0.1962-0.3457-0.10830.23080.05150.06420.4465-0.01210.276-2.87560.2914-8.2448
24.0527-0.1037-0.2080.95330.13211.44330.061-0.12330.26770.0668-0.0274-0.259-0.25220.0221-0.02970.2415-0.020.01030.2677-0.06960.161318.816960.645-16.7648
30.7131-0.006-0.22910.3797-0.01230.73450.0336-0.04730.02860.00870.01240.1032-0.0611-0.2032-0.05510.15420.00640.00350.23510.00010.19159.433653.1873-24.1107
42.3050.1985-0.09922.51431.01641.62660.0115-0.1205-0.25740.1454-0.10890.28080.362-0.49850.09920.2633-0.1590.00160.40230.01760.3218-4.667726.9469-27.5435
51.37370.13820.44870.81240.23861.29670.0209-0.10160.01840.1309-0.11110.28320.1089-0.75150.05070.2283-0.09270.04220.6498-0.00890.3975-13.99336.8452-16.7184
61.12460.2373-0.37530.43220.19221.26010.02080.19-0.0931-0.0827-0.08990.23350.1297-0.60410.06610.2317-0.0928-0.04410.4525-0.01460.3001-3.890932.7836-37.8028
70.68880.43-0.12161.0816-0.35550.81960.0373-0.00640.0622-0.05650.00190.09-0.0965-0.1414-0.02270.19970.02170.00690.2148-0.01360.236417.933653.7013-37.884
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 42 )A2 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 81 )A43 - 81
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 265 )A82 - 265
4X-RAY DIFFRACTION4chain 'A' and (resid 266 through 311 )A266 - 311
5X-RAY DIFFRACTION5chain 'A' and (resid 312 through 370 )A312 - 370
6X-RAY DIFFRACTION6chain 'A' and (resid 371 through 440 )A371 - 440
7X-RAY DIFFRACTION7chain 'A' and (resid 441 through 490 )A441 - 490

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