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- PDB-4f3x: Crystal structure of putative aldehyde dehydrogenase from Sinorhi... -

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Basic information

Entry
Database: PDB / ID: 4f3x
TitleCrystal structure of putative aldehyde dehydrogenase from Sinorhizobium meliloti 1021 complexed with NAD
ComponentsPutative aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
Aminobutyraldehyde 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal ...Aminobutyraldehyde 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 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of putative aldehyde dehydrogenase from Sinorhizobium meliloti 1021 complexed with NAD
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative aldehyde dehydrogenase
B: Putative aldehyde dehydrogenase
C: Putative aldehyde dehydrogenase
D: Putative aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,24413
Polymers218,1304
Non-polymers3,1149
Water11,566642
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24030 Å2
ΔGint-128 kcal/mol
Surface area57310 Å2
MethodPISA
2
A: Putative aldehyde dehydrogenase
B: Putative aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6687
Polymers109,0652
Non-polymers1,6035
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-50 kcal/mol
Surface area33090 Å2
MethodPISA
3
C: Putative aldehyde dehydrogenase
D: Putative aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5766
Polymers109,0652
Non-polymers1,5114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-45 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.438, 96.905, 121.811
Angle α, β, γ (deg.)90.000, 89.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative aldehyde dehydrogenase /


Mass: 54532.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R02268, SMc01656 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: Q92ND9, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 642 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M ammonium acetate, 0.1M Bis-Tris-HCl, pH 5.5, 25% PEG3350. Overnight soak with 10mM NAD, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 126866 / % possible obs: 95.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.095 / Χ2: 1.336 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.01-2.042.30.80646490.873170.2
2.04-2.082.50.82951710.947178.4
2.08-2.122.60.83956090.858185.3
2.12-2.172.80.74560320.933191.2
2.17-2.2130.70662160.943195
2.21-2.263.10.68365000.991198.1
2.26-2.323.30.61965221.01199.1
2.32-2.383.40.54465931.003199.9
2.38-2.453.50.47265531.068199.9
2.45-2.533.50.42866461.068199.9
2.53-2.623.50.34565771.135199.9
2.62-2.733.50.28966111.22199.9
2.73-2.853.50.21866041.297199.8
2.85-33.50.17565981.398199.8
3-3.193.50.13165911.603199.8
3.19-3.443.50.09866281.752199.9
3.44-3.783.60.07666552.075199.9
3.78-4.333.60.06166532.221199.9
4.33-5.453.50.04266681.644199.9
5.45-503.70.03667901.516199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.14 Å
Translation2.5 Å44.14 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DAL

4dal


Resolution: 2.01→19.91 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2121 / WRfactor Rwork: 0.1637 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8078 / SU B: 11.607 / SU ML: 0.147 / SU R Cruickshank DPI: 0.1903 / SU Rfree: 0.1721 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 6378 5 %RANDOM
Rwork0.1802 ---
obs0.1828 126673 95.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 233.15 Å2 / Biso mean: 51.1832 Å2 / Biso min: 23.01 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.01→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14420 0 206 642 15268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01914971
X-RAY DIFFRACTIONr_angle_refined_deg1.321.97420367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19751915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09123.932646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.605152249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.37315106
X-RAY DIFFRACTIONr_chiral_restr0.0870.22308
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111346
LS refinement shellResolution: 2.008→2.059 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 326 -
Rwork0.355 6461 -
all-6787 -
obs--69.98 %
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)
10.75820.00590.36220.3276-0.1011.1045-0.0371-0.1733-0.06140.07960.04930.0004-0.0501-0.2824-0.01210.15560.02580.03180.08620.00110.0968-29.685915.5651-2.7778
20.79960.37920.28410.45630.24430.5821-0.1360.14740.1194-0.03210.1288-0.0225-0.17090.06890.00720.1751-0.01190.00930.0423-0.00640.1262-8.069736.2139-23.7309
31.02940.07930.53530.35260.11830.9372-0.04490.21250.0417-0.10590.05570.0593-0.0752-0.015-0.01070.1121-0.02750.02730.08430.01650.0383-37.137214.31-51.1304
40.27960.2260.27240.59330.04110.60210.03990.1208-0.2081-0.02590.0649-0.14360.18370.0663-0.10480.18990.00170.02570.0731-0.11650.2081-14.6162-10.2412-37.1814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 787
2X-RAY DIFFRACTION2B0 - 770
3X-RAY DIFFRACTION3C0 - 765
4X-RAY DIFFRACTION4D1 - 720

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