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- PDB-5nno: Structure of TbALDH3 complexed with NAD and AN3057 aldehyde -

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Basic information

Entry
Database: PDB / ID: 5nno
TitleStructure of TbALDH3 complexed with NAD and AN3057 aldehyde
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / ALDH / Trypanosoma brucei / glycosomal / oxaborole / NAD
Function / homology
Function and homology information


cellular aldehyde metabolic process / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
Aldehyde dehydrogenase NAD(P)-dependent / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal ...Aldehyde dehydrogenase NAD(P)-dependent / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-92N / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZoltner, M. / Zhang, N. / Horn, D. / Field, M.C.
CitationJournal: PLoS Pathog. / Year: 2018
Title: Host-parasite co-metabolic activation of antitrypanosomal aminomethyl-benzoxaboroles.
Authors: Zhang, N. / Zoltner, M. / Leung, K.F. / Scullion, P. / Hutchinson, S. / Del Pino, R.C. / Vincent, I.M. / Zhang, Y.K. / Freund, Y.R. / Alley, M.R.K. / Jacobs, R.T. / Read, K.D. / Barrett, M.P. ...Authors: Zhang, N. / Zoltner, M. / Leung, K.F. / Scullion, P. / Hutchinson, S. / Del Pino, R.C. / Vincent, I.M. / Zhang, Y.K. / Freund, Y.R. / Alley, M.R.K. / Jacobs, R.T. / Read, K.D. / Barrett, M.P. / Horn, D. / Field, M.C.
History
DepositionApr 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7616
Polymers119,9262
Non-polymers1,8354
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11510 Å2
ΔGint-41 kcal/mol
Surface area35720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.168, 62.524, 92.974
Angle α, β, γ (deg.)90.00, 100.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 6 - 489 / Label seq-ID: 6 - 489

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Aldehyde dehydrogenase / TbALDH3


Mass: 59962.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: TbgDal_VI2840,Tb427.06.3050 / Production host: Escherichia coli (E. coli) / References: UniProt: C9ZQX6
#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-92N / 4-[(1-oxidanyl-3~{H}-2,1-benzoxaborol-5-yl)oxy]benzaldehyde


Mass: 254.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11BO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 100 mM Bis-Tris pH 5.5, 0.2 M LiSO4, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.862
11L, -K, H20.138
ReflectionResolution: 2.5→46.56 Å / Num. obs: 34306 / % possible obs: 97.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 7.8 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 8 / Num. unique obs: 3730 / CC1/2: 0.968 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MYP

5myp


Resolution: 2.5→46.56 Å / Cor.coef. Fo:Fc: 0.827 / Cor.coef. Fo:Fc free: 0.76 / SU B: 26.014 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.075
Details: INTENSITY BASED TWIN REFINEMENT HAS BEEN USED; HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27807 1736 5.1 %RANDOM
Rwork0.23389 ---
obs0.23613 32560 85.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.145 Å2
Baniso -1Baniso -2Baniso -3
1--7.85 Å20 Å2-4.06 Å2
2---13.22 Å20 Å2
3---21.07 Å2
Refinement stepCycle: 1 / Resolution: 2.5→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7512 0 126 200 7838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197904
X-RAY DIFFRACTIONr_bond_other_d0.0020.027574
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.98810750
X-RAY DIFFRACTIONr_angle_other_deg0.991317538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6515988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39923.83329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.188151378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9811559
X-RAY DIFFRACTIONr_chiral_restr0.0820.21242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021562
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.040.2013927
X-RAY DIFFRACTIONr_mcbond_other0.0410.2023928
X-RAY DIFFRACTIONr_mcangle_it00.34922
X-RAY DIFFRACTIONr_mcangle_other0.0160.3014923
X-RAY DIFFRACTIONr_scbond_it0.2410.2723977
X-RAY DIFFRACTIONr_scbond_other0.2410.2723978
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3460.4115829
X-RAY DIFFRACTIONr_long_range_B_refined1.9672.7488426
X-RAY DIFFRACTIONr_long_range_B_other1.9542.7158410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 30730 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 128 -
Rwork0.311 2260 -
obs--93.5 %
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)
11.3541-1.0481-0.30541.44570.30182.3653-0.1412-0.06640.01820.11160.0417-0.00040.3063-0.02080.09940.42430.0007-0.01860.1870.02660.024385.9981-15.8237136.1067
20.2044-0.09450.38450.71860.46922.32770.03690.0547-0.1327-0.11320.3162-0.22450.01480.3915-0.35320.48180.00660.01570.338-0.11670.26891.6223-8.0158122.7223
30.4595-0.06280.20370.59110.0161.16430.01890.0618-0.019-0.07340.02070.02090.112-0.025-0.03960.36960.0112-0.00410.2386-0.01430.003380.3131-1.412120.6378
41.66981.2926-0.98053.62790.78691.6490.1586-0.03360.3542-0.0062-0.09930.6483-0.0193-0.1312-0.05930.3625-0.0228-0.05090.35650.00280.161866.5195-0.8946107.05
51.2789-0.33780.81370.6038-0.40121.6643-0.00930.139-0.0094-0.06350.00160.0032-0.13770.07890.00770.3758-0.02510.03640.2347-0.01140.004986.691312.4628120.5049
61.78190.38321.48211.4186-0.35621.60780.22370.0802-0.40930.1137-0.1452-0.76040.03740.1261-0.07850.6434-0.02260.13060.40040.05070.5353108.281927.6774162.543
72.866-0.0612-0.67071.70460.18143.9561-0.11790.18960.3869-0.08950.04610.0569-0.2309-0.09290.07180.3010.00320.01580.12180.01470.09184.146831.7895136.3957
80.4596-0.09790.38820.6853-0.03131.0141-0.0159-0.01830.03920.0696-0.0051-0.0553-0.04650.06740.0210.3388-0.00990.00650.24370.00090.007292.632819.9592149.9794
92.32110.3125-0.26330.16930.52433.5063-0.0051-0.1865-0.1860.0910.00460.0027-0.0705-0.04690.00040.46510.00770.02280.31480.0250.085690.472422.7623176.7286
100.53750.0842-0.2181.2182-0.00482.11080.0004-0.1252-0.16470.4213-0.13620.51580.410.00750.13570.601-0.02780.08170.35530.00050.334590.75735.7106171.3013
110.55110.37220.4660.4934-0.20671.53020.08170.0725-0.0794-0.0085-0.0888-0.08940.19860.31560.00710.36160.0672-0.00050.2623-0.0270.052598.04475.8308146.9946
122.7486-2.92911.82443.1648-1.95331.22-0.0990.03940.3649-0.0097-0.1222-0.5042-0.03430.10480.22120.81880.04150.06030.7078-0.00990.434791.7008-7.9189103.8828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 55
2X-RAY DIFFRACTION2A56 - 104
3X-RAY DIFFRACTION3A105 - 306
4X-RAY DIFFRACTION4A307 - 348
5X-RAY DIFFRACTION5A349 - 468
6X-RAY DIFFRACTION6A469 - 489
7X-RAY DIFFRACTION7B6 - 44
8X-RAY DIFFRACTION8B45 - 285
9X-RAY DIFFRACTION9B286 - 329
10X-RAY DIFFRACTION10B330 - 382
11X-RAY DIFFRACTION11B383 - 463
12X-RAY DIFFRACTION12B464 - 489

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