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- PDB-5n5s: Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Phys... -

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Basic information

Entry
Database: PDB / ID: 5n5s
TitleCrystal structure of aldehyde dehydrogenase 21 (ALDH21) from Physcomitrella patens in complex with NADP+
ComponentsAldehyde dehydrogenase 21 (ALDH21)
KeywordsOXIDOREDUCTASE / Rossmann fold / succinic semialdehyde dehydrogenase / NADP+ binding
Function / homology
Function and homology information


lactaldehyde dehydrogenase activity / glyceraldehyde-3-phosphate dehydrogenase (NADP+)
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesPhyscomitrella patens subsp. patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKopecny, D. / Vigouroux, A. / Briozzo, P. / Morera, S.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
GACR15-22322S Czech Republic
CitationJournal: Plant J. / Year: 2017
Title: The ALDH21 gene found in lower plants and some vascular plants codes for a NADP(+) -dependent succinic semialdehyde dehydrogenase.
Authors: Kopecna, M. / Vigouroux, A. / Vilim, J. / Koncitikova, R. / Briozzo, P. / Hajkova, E. / Jaskova, L. / von Schwartzenberg, K. / Sebela, M. / Morera, S. / Kopecny, D.
History
DepositionFeb 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase 21 (ALDH21)
B: Aldehyde dehydrogenase 21 (ALDH21)
C: Aldehyde dehydrogenase 21 (ALDH21)
D: Aldehyde dehydrogenase 21 (ALDH21)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,71111
Polymers226,5514
Non-polymers3,1607
Water3,153175
1
A: Aldehyde dehydrogenase 21 (ALDH21)
B: Aldehyde dehydrogenase 21 (ALDH21)
hetero molecules

A: Aldehyde dehydrogenase 21 (ALDH21)
B: Aldehyde dehydrogenase 21 (ALDH21)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,64910
Polymers226,5514
Non-polymers3,0986
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,-y,z1
Buried area24290 Å2
ΔGint-88 kcal/mol
Surface area60130 Å2
MethodPISA
2
C: Aldehyde dehydrogenase 21 (ALDH21)
D: Aldehyde dehydrogenase 21 (ALDH21)
hetero molecules

C: Aldehyde dehydrogenase 21 (ALDH21)
D: Aldehyde dehydrogenase 21 (ALDH21)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,77312
Polymers226,5514
Non-polymers3,2228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area25050 Å2
ΔGint-78 kcal/mol
Surface area59850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.380, 165.280, 138.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Aldehyde dehydrogenase 21 (ALDH21)


Mass: 56637.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrella patens subsp. patens (plant)
Gene: PHYPADRAFT_215149 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A9SS48
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: protein buffer: 20 mM Tris-HCl buffer pH 8.0, 100 mM NaCl, 1 mM NADP+; precipitant solution: 35% (w/v) PEG 2000-MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 91956 / % possible obs: 99.5 % / Redundancy: 12.9 % / Biso Wilson estimate: 68.55 Å2 / CC1/2: 0.999 / Rsym value: 0.099 / Net I/σ(I): 15.1
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 14371 / CC1/2: 0.772 / % possible all: 97.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MZ5

5mz5


Resolution: 2.3→46.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.285 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.194
RfactorNum. reflection% reflectionSelection details
Rfree0.207 4579 5 %RANDOM
Rwork0.183 ---
obs0.185 91565 99.9 %-
Displacement parametersBiso mean: 83.67 Å2
Baniso -1Baniso -2Baniso -3
1-12.868 Å20 Å20 Å2
2---1.2507 Å20 Å2
3----11.6173 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.3→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14866 0 204 175 15245
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00915387HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.120846HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5411SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes376HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2282HARMONIC5
X-RAY DIFFRACTIONt_it15387HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion18.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1998SEMIHARMONIC5
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_contact17694SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 335 5 %
Rwork0.256 6366 -
all0.258 6701 -
obs--99.84 %
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)
11.6701-0.0620.03950.95170.06020.9055-0.1087-0.18340.45470.2135-0.06510.1619-0.2451-0.16420.1737-0.2120.1221-0.0253-0.0997-0.06810.0367122.92820.07026.7018
21.6460.0897-0.06661.04990.16680.6537-0.03160.53180.4161-0.3247-0.0574-0.1531-0.25880.1350.089-0.21880.0626-0.01120.06980.1977-0.047144.52919.9118-23.1896
32.0757-0.36480.08241.7762-0.50441.90950.11150.14320.59410.07280.16270.3176-0.3484-0.3209-0.2742-0.34640.07290.0934-0.56190.1097-0.150274.960720.4478-87.1922
42.0164-0.69510.67971.9602-0.06561.671-0.3277-0.46080.79230.70160.2716-0.7867-0.47820.17510.0561-0.0843-0.0052-0.2655-0.4884-0.2594-0.0421104.6519.3274-65.5492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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