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- PDB-5mz8: Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Phys... -

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Basic information

Entry
Database: PDB / ID: 5mz8
TitleCrystal structure of aldehyde dehydrogenase 21 (ALDH21) from Physcomitrella patens in complex with the reaction product succinate
Componentsaldehyde dehydrogenase 21
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
DI(HYDROXYETHYL)ETHER / SUCCINIC ACID / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesPhyscomitrella patens subsp. patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionJan 31, 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 / 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
B: aldehyde dehydrogenase 21
C: aldehyde dehydrogenase 21
D: aldehyde dehydrogenase 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,68060
Polymers226,5514
Non-polymers4,12856
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31630 Å2
ΔGint80 kcal/mol
Surface area59340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.580, 151.810, 159.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
aldehyde dehydrogenase 21 /


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: Physcomitrella patens (plant) / References: UniProt: A9SS48

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Non-polymers , 5 types, 704 molecules

#2: Chemical
ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
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 and 2% (w/v) glycerol; precipitant solution: 29 % (w/v) PEG 2000-MME, soak with 20 mM sodium succinate for 1 hour

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→55 Å / Num. obs: 112964 / % possible obs: 100 % / Redundancy: 9.64 % / Biso Wilson estimate: 36.68 Å2 / Rsym value: 0.28 / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 9.82 % / Mean I/σ(I) obs: 1.32 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W8Q

2w8q


Resolution: 2.2→50.07 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.233 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.22 5648 5 %RANDOM
Rwork0.188 ---
obs0.189 112956 100 %-
Displacement parametersBiso mean: 37.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.678 Å20 Å20 Å2
2---1.7462 Å20 Å2
3---2.4242 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→50.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14873 0 269 648 15790
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00915390HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1220699HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5415SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes376HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2191HARMONIC5
X-RAY DIFFRACTIONt_it15390HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion16.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1967SEMIHARMONIC5
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_contact18194SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 410 5 %
Rwork0.23 7797 -
all0.231 8207 -
obs--99.67 %
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)
10.31990.0219-0.02180.2913-0.00970.32580.00220.04930.0259-0.0609-0.0067-0.0394-0.01910.04560.0044-0.1062-0.00530.00950.12540.0173-0.10147.4584-71.378539.8184
20.2534-0.02570.08620.2334-0.02140.31470.00420.0132-0.0199-0.04760.01020.04060.0384-0.0464-0.0144-0.0922-0.00130.00870.12070.0135-0.094317.0746-91.360645.4189
30.2253-0.05010.0950.4006-0.05640.3330.003-0.05050.00910.06570.0009-0.02580.00970.0518-0.0039-0.11040.00470.0030.144-0.0109-0.111347.4343-80.940183.4841
40.26380.0010.00910.1429-0.02490.4175-0.014-0.08850.07190.03970.00860.0111-0.0805-0.10070.0054-0.11250.04-0.00180.1388-0.0406-0.095217.6238-60.578978.0831
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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