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- PDB-4pxl: Structure of Zm ALDH2-3 (RF2C) in complex with NAD -

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Basic information

Entry
Database: PDB / ID: 4pxl
TitleStructure of Zm ALDH2-3 (RF2C) in complex with NAD
Components(Cytosolic aldehyde dehydrogenase ...) x 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding
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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Cytosolic aldehyde dehydrogenase RF2C / Aldehyde dehydrogenase3
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMorera, S. / Vigouroux, A. / Kopecny, D.
CitationJournal: Biochem.J. / Year: 2015
Title: Role and structural characterization of plant aldehyde dehydrogenases from family 2 and family 7.
Authors: Koncitikova, R. / Vigouroux, A. / Kopecna, M. / Andree, T. / Bartos, J. / Sebela, M. / Morera, S. / Kopecny, D.
History
DepositionMar 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosolic aldehyde dehydrogenase RF2C
B: Cytosolic aldehyde dehydrogenase RF2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,07720
Polymers111,6812
Non-polymers2,39618
Water4,666259
1
A: Cytosolic aldehyde dehydrogenase RF2C
B: Cytosolic aldehyde dehydrogenase RF2C
hetero molecules

A: Cytosolic aldehyde dehydrogenase RF2C
B: Cytosolic aldehyde dehydrogenase RF2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,15340
Polymers223,3614
Non-polymers4,79236
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area32310 Å2
ΔGint-104 kcal/mol
Surface area56420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.860, 126.080, 78.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Cytosolic aldehyde dehydrogenase ... , 2 types, 2 molecules AB

#1: Protein Cytosolic aldehyde dehydrogenase RF2C


Mass: 55848.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: rf2c / Plasmid: pCDFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PlysS / References: UniProt: Q8S531, UniProt: Q8S532*PLUS
#2: Protein Cytosolic aldehyde dehydrogenase RF2C


Mass: 55832.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: rf2c / Plasmid: pCDFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PlysS / References: UniProt: Q8S531, UniProt: Q8S532*PLUS

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Non-polymers , 6 types, 277 molecules

#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CORRECT SEQUENCE HAS BEEN DEPOSITED IN GENBANK, KJ004512. THE SEQUENCE COMES FROM A CULTIVAR ...THE CORRECT SEQUENCE HAS BEEN DEPOSITED IN GENBANK, KJ004512. THE SEQUENCE COMES FROM A CULTIVAR WHICH IS DIFFERENT FROM THAT WHICH HAS GIVEN THE SEQUENCE IN THE DATABASE

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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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 400, 0.2 M Cacl2, 0.1 M Acetate Sodium, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→49.1 Å / Num. all: 54000 / Num. obs: 52406 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 41.47 Å2
Reflection shellResolution: 2.25→2.38 Å / % possible all: 99

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→49.1 Å / Cor.coef. Fo:Fc: 0.9456 / Cor.coef. Fo:Fc free: 0.9293 / SU R Cruickshank DPI: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 2615 5 %RANDOM
Rwork0.1706 ---
obs0.1723 52295 99.94 %-
all-54000 --
Displacement parametersBiso mean: 42.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.7253 Å20 Å20 Å2
2--10.9491 Å20 Å2
3----10.2238 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 2.25→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7397 0 155 259 7811
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017708HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1110447HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2610SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes168HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1168HARMONIC5
X-RAY DIFFRACTIONt_it7708HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion17.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1001SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9328SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2373 190 5 %
Rwork0.207 3613 -
all0.2085 3803 -
obs--99.94 %
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)
10.62990.17730.12160.70770.04820.15050.0021-0.0798-0.06780.0506-0.0115-0.2604-0.01040.01550.0094-0.1072-0.0016-0.0057-0.09530.0177-0.0388-32.7891-4.934845.532
20.42280.10880.17750.98010.08310.05970.0110.1195-0.1448-0.26540.0171-0.08380.0080.039-0.0281-0.0294-0.0060.0384-0.0848-0.0375-0.1072-46.8355-21.257417.2192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|17 - A|502 A|601 - A|601 }A17 - 502
2X-RAY DIFFRACTION1{ A|17 - A|502 A|601 - A|601 }A601
3X-RAY DIFFRACTION2{ B|17 - B|502 B|601 - B|601 }B17 - 502
4X-RAY DIFFRACTION2{ B|17 - B|502 B|601 - B|601 }B601

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