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- PDB-5mz5: Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Phys... -

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Basic information

Entry
Database: PDB / ID: 5mz5
TitleCrystal structure of aldehyde dehydrogenase 21 (ALDH21) from Physcomitrella patens in its apoform
ComponentsALDH21)
KeywordsOXIDOREDUCTASE / Rossmann fold / succinic semialdehyde dehydrogenase / NADP+ binding
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) / lactaldehyde dehydrogenase (NAD+) activity / 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 domain / Aldehyde dehydrogenase family / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesPhyscomitrella patens subsp. patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKopecny, D. / Koncitikova, R. / 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 30, 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: ALDH21)
B: ALDH21)
C: ALDH21)
D: ALDH21)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,55129
Polymers226,5514
Non-polymers2,00025
Water16,214900
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25100 Å2
ΔGint-33 kcal/mol
Surface area59470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.802, 151.793, 158.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
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 / Plasmid: pCDFDuet / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A9SS48
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 900 / 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: 49.54 %
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: 30 % (w/v) PEG 2000-MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 120186 / % possible obs: 98.6 % / Redundancy: 6.41 % / Biso Wilson estimate: 36.94 Å2 / Rsym value: 0.139 / Net I/σ(I): 10.46
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.24 % / Mean I/σ(I) obs: 1.36 / Rsym value: 0.8 / % possible all: 91.2

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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: 2.15→48.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.215 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.21 5992 5 %RANDOM
Rwork0.184 ---
obs0.186 119834 99.2 %-
Displacement parametersBiso mean: 34.43 Å2
Baniso -1Baniso -2Baniso -3
1--2.3562 Å20 Å20 Å2
2---3.9809 Å20 Å2
3---6.3371 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.15→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14866 0 130 900 15896
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115275HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1120612HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5359SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes376HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2182HARMONIC5
X-RAY DIFFRACTIONt_it15275HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion16.77
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1966SEMIHARMONIC5
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_contact18605SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 405 5 %
Rwork0.25 7698 -
all0.252 8103 -
obs--91.79 %
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)
10.35410.0133-0.10230.37710.0350.48650.00330.04230.039-0.09020.0089-0.0383-0.05010.0641-0.01220.0008-0.01550.0101-0.03530.0091-0.089347.8978-71.248439.508
20.2672-0.02770.08710.3083-0.02190.3730.00750.0126-0.0376-0.0386-0.00080.04870.0587-0.0635-0.00670.0008-0.01640.011-0.01370.0005-0.082117.2908-91.254545.1602
30.26420.00990.11770.43010.03920.43430.0114-0.03130.00320.09680.0007-0.04840.02640.0609-0.0121-0.00390.0118-0.0091-0.0232-0.0092-0.087947.8736-80.890683.3932
40.32160.0108-0.07340.2080.03710.3841-0.0055-0.04210.10230.0301-0.00270.0093-0.0875-0.10310.0082-0.00880.0419-0.014-0.0146-0.0255-0.069417.8285-60.082377.8294
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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