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- PDB-4dng: Crystal structure of putative aldehyde dehydrogenase from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 4dng
TitleCrystal structure of putative aldehyde dehydrogenase from Bacillus subtilis subsp. subtilis str. 168
ComponentsUncharacterized aldehyde dehydrogenase AldY
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity
Similarity search - Function
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 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
Putative aldehyde dehydrogenase AldY
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of putative aldehyde dehydrogenase from Bacillus subtilis subsp. subtilis str. 168
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized aldehyde dehydrogenase AldY
B: Uncharacterized aldehyde dehydrogenase AldY


Theoretical massNumber of molelcules
Total (without water)105,7542
Polymers105,7542
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-14 kcal/mol
Surface area35480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.205, 90.522, 86.863
Angle α, β, γ (deg.)90.000, 108.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized aldehyde dehydrogenase AldY


Mass: 52876.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: subtilis str. 168 / Gene: aldY, BSU38830, CAB15909.1, yxkE / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: P94358, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M ammonium acetate, 0.1M Tris, pH 8.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 41160 / % possible obs: 97.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 / Χ2: 1.692 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.343.20.82417200.754183
2.34-2.3840.85220290.731195
2.38-2.435.10.81120300.752199.6
2.43-2.485.50.73221110.7681100
2.48-2.535.70.62620940.7991100
2.53-2.595.70.50820940.8131100
2.59-2.665.70.4120890.8771100
2.66-2.735.70.32221000.8931100
2.73-2.815.70.24820911.0131100
2.81-2.95.70.20721081.1071100
2.9-35.70.16920861.1921100
3-3.125.70.13321051.4531100
3.12-3.265.60.10420961.6351100
3.26-3.445.60.08820872.103199.9
3.44-3.655.60.07621002.4241100
3.65-3.935.50.06721132.81199.5
3.93-4.335.30.06220603.211198.1
4.33-4.955.10.0620053.599194.8
4.95-6.245.20.05620763.39198.1
6.24-504.90.0519663.521190.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.99 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.2 Å
Translation2.5 Å41.2 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R64

3r64


Resolution: 2.5→19.84 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2609 / WRfactor Rwork: 0.1845 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8073 / SU B: 23.487 / SU ML: 0.241 / SU R Cruickshank DPI: 0.7387 / SU Rfree: 0.3119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.739 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 1631 5.1 %RANDOM
Rwork0.1816 ---
obs0.1852 32292 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 196.36 Å2 / Biso mean: 82.637 Å2 / Biso min: 19.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6888 0 0 70 6958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.027017
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.969494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11525.428304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.331151253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2151533
X-RAY DIFFRACTIONr_chiral_restr0.0950.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215205
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 124 -
Rwork0.262 2198 -
all-2322 -
obs--100 %
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)
11.88370.4834-0.01161.8020.15391.5922-0.17730.2301-0.2773-0.2880.10520.1103-0.1095-0.06940.07210.10070.02050.00920.1133-0.03530.0735-4.811721.0084-30.1374
20.98220.1899-0.50131.5510.34481.7860.02680.07950.0249-0.2948-0.06630.3931-0.166-0.14760.03950.16690.0717-0.04980.09410.01110.1124-7.851553.9815-10.6126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 478
2X-RAY DIFFRACTION2B1 - 478

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