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- PDB-3ty7: Crystal Structure of Aldehyde Dehydrogenase family Protein from S... -

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Basic information

Entry
Database: PDB / ID: 3ty7
TitleCrystal Structure of Aldehyde Dehydrogenase family Protein from Staphylococcus aureus
ComponentsPutative aldehyde dehydrogenase SAV2122
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / alpha-beta sandwich / cytosol
Function / homology
Function and homology information


cellular aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity
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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...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, 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Putative aldehyde dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKim, Y. / Joachimiak, G. / Jedrzejczak, R. / Rubin, E. / Ioerger, T. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: Crystal Structure of Aldehyde Dehydrogenase family Protein from Staphylococcus aureus
Authors: Kim, Y. / Joachimiak, G. / Jedrzejczak, R. / Rubin, E. / Ioerger, T. / Sacchettini, J. / Joachimiak, A.
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative aldehyde dehydrogenase SAV2122
B: Putative aldehyde dehydrogenase SAV2122
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,14112
Polymers105,2602
Non-polymers88110
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-14 kcal/mol
Surface area35670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.448, 173.448, 96.569
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Detailsa dimer in the asymmetric unit

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Components

#1: Protein Putative aldehyde dehydrogenase SAV2122


Mass: 52630.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: aureus Mu50 / Gene: SAV2122 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q99SD6, aldehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5, 30 % PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 8, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 42456 / Num. obs: 42456 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 55.13 Å2 / Rsym value: 0.057 / Net I/σ(I): 16.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 2075 / Rsym value: 0.582 / % possible all: 98.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: dev_851)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→32.456 Å / SU ML: 0.74 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.99 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2129 5.04 %random
Rwork0.185 ---
all0.186 42206 --
obs0.186 42206 99.62 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.489 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 65 Å2
Baniso -1Baniso -2Baniso -3
1--2.2325 Å2-0 Å20 Å2
2---2.2325 Å2-0 Å2
3---4.4649 Å2
Refinement stepCycle: LAST / Resolution: 2.4→32.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6963 0 57 163 7183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037196
X-RAY DIFFRACTIONf_angle_d0.8779714
X-RAY DIFFRACTIONf_dihedral_angle_d14.0762697
X-RAY DIFFRACTIONf_chiral_restr0.0671080
X-RAY DIFFRACTIONf_plane_restr0.0041281
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4-2.45590.35381400.3092643278398
2.4559-2.51730.28721500.27562670282099
2.5173-2.58530.31241570.26722630278799
2.5853-2.66130.28421610.246526462807100
2.6613-2.74720.26661500.233626572807100
2.7472-2.84530.25721280.228527202848100
2.8453-2.95920.27531360.22526502786100
2.9592-3.09370.26911160.217727182834100
3.0937-3.25670.24541300.208726732803100
3.2567-3.46050.24091580.19926582816100
3.4605-3.72740.2211390.185727032842100
3.7274-4.10180.18161510.169726592810100
4.1018-4.69380.15361500.140326842834100
4.6938-5.90790.18421360.158826872823100
5.9079-32.4590.17941270.16112679280699
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)
13.8084-0.60070.49482.7103-0.54222.1419-0.02370.35730.1136-0.062-0.02590.1795-0.08990.24770.05320.2969-0.0077-0.12390.25110.01820.268653.356837.30546.0684
24.73982.32671.03373.5390.94998.0766-0.04740.5884-1.5179-0.994-0.0260.17131.3331-0.125-0.04720.82560.0798-0.14180.4289-0.13180.970948.098620.152345.8918
35.06730.38640.79672.2651-0.55853.9732-0.1720.1209-0.1988-0.0168-0.0244-0.12430.33760.45660.18790.40750.09480.14110.53410.05410.334353.217628.355815.2713
40.16830.0975-1.23811.0914-0.53325.4597-0.06050.22730.31790.0774-0.044-0.0012-0.2567-0.37780.19680.29670.05250.020.44360.04780.634532.119231.619832.9676
51.77341.1417-0.1264.3358-0.83991.65820.1540.0883-0.06280.12520.05970.26840.1345-0.2153-0.19820.23520.0295-0.02480.2508-0.05440.280620.57747.383437.68
65.2621.167-1.82975.4146-0.15977.84150.0698-0.99120.48651.4372-0.0843-1.5087-0.50060.97030.01510.56470.0186-0.21830.5609-0.18840.812737.54088.886639.4033
71.4890.74371.60732.35610.0781.9550.0632-0.10620.39620.26780.30980.55920.26-0.2098-0.10820.5013-0.03220.08520.3844-0.08450.618427.45316.069960.8684
82.7287-0.21731.92093.6345-0.11143.03260.3653-0.32290.14480.5614-0.1999-0.11410.2378-0.2381-0.18390.6809-0.12520.10150.43650.05590.400328.42878.377169.7628
91.0959-0.1764-0.0620.8954-1.38914.70050.05910.03860.10810.22670.06780.1022-0.3807-0.32180.07690.37240.04290.11830.2303-0.02690.678827.559829.07648.9773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:212)
2X-RAY DIFFRACTION2chain 'A' and (resseq 213:240)
3X-RAY DIFFRACTION3chain 'A' and (resseq 241:415)
4X-RAY DIFFRACTION4chain 'A' and (resseq 416:475)
5X-RAY DIFFRACTION5chain 'B' and (resseq 0:206)
6X-RAY DIFFRACTION6chain 'B' and (resseq 207:234)
7X-RAY DIFFRACTION7chain 'B' and (resseq 235:276)
8X-RAY DIFFRACTION8chain 'B' and (resseq 277:415)
9X-RAY DIFFRACTION9chain 'B' and (resseq 416:475)

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