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- PDB-7kqv: Crystal Structure of aldehyde dehydrogenase (ChALDH) from Cladosp... -

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Basic information

Entry
Database: PDB / ID: 7kqv
TitleCrystal Structure of aldehyde dehydrogenase (ChALDH) from Cladosporium herbarum
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde dehydrogenase / ChALDH / Cladosporium herbarum
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Aldehyde dehydrogenase
Similarity search - Component
Biological speciesCladosporium herbarum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsLee, S.G. / Jez, J.M.
CitationJournal: Transgenic Res / Year: 2022
Title: Biochemical and clinical studies of putative allergens to assess what distinguishes them from other non-allergenic proteins in the same family.
Authors: Glenn, K.C. / Silvanovich, A. / Lee, S.G. / Allen, A. / Park, S. / Dunn, S.E. / Kessenich, C. / Meng, C. / Vicini, J.L. / Jez, J.M.
History
DepositionNov 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)214,4514
Polymers214,4514
Non-polymers00
Water0
1
A: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase

B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)214,4514
Polymers214,4514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455-x-1/2,-y+1/2,z+1/21
Buried area16750 Å2
ΔGint-72 kcal/mol
Surface area59730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.180, 157.180, 164.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Aldehyde dehydrogenase / / ALDH / Allergen Cla h 3 / Allergen Cla h III


Mass: 53612.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cladosporium herbarum (fungus) / Gene: CLAH10, CLAH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P40108, aldehyde dehydrogenase (NAD+)

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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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% PEG 100, 100 mM sodium/potassium phosphate, pH 6.2, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 33530 / % possible obs: 100 % / Redundancy: 2.9 % / Biso Wilson estimate: 79.3 Å2 / Rpim(I) all: 0.082 / Rrim(I) all: 0.203 / Net I/σ(I): 15.9
Reflection shellResolution: 3.19→3.24 Å / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1643 / CC1/2: 0.842 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.14_3260refinement
Cootmodel building
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fhz

5fhz


Resolution: 3.18→49.7 Å / SU ML: 0.3571 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.8598 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.281 1692 5.06 %
Rwork0.233 31756 -
obs0.2356 33448 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.75 Å2
Refinement stepCycle: LAST / Resolution: 3.18→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13484 0 0 0 13484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010813748
X-RAY DIFFRACTIONf_angle_d1.352718620
X-RAY DIFFRACTIONf_chiral_restr0.07312113
X-RAY DIFFRACTIONf_plane_restr0.00792395
X-RAY DIFFRACTIONf_dihedral_angle_d5.75568130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.270.35121170.28962633X-RAY DIFFRACTION97.48
3.27-3.380.28221590.26352614X-RAY DIFFRACTION99.71
3.38-3.50.31611360.23912616X-RAY DIFFRACTION99.64
3.5-3.640.29541370.23962670X-RAY DIFFRACTION99.79
3.64-3.810.33111380.23842622X-RAY DIFFRACTION99.89
3.81-4.010.30961370.23012644X-RAY DIFFRACTION99.96
4.01-4.260.2881400.22862652X-RAY DIFFRACTION99.93
4.26-4.590.25451460.19562658X-RAY DIFFRACTION99.93
4.59-5.050.221430.19842659X-RAY DIFFRACTION99.89
5.05-5.780.29371380.24582659X-RAY DIFFRACTION99.96
5.78-7.270.32391440.26712682X-RAY DIFFRACTION99.96
7.27-49.70.2561570.22872647X-RAY DIFFRACTION98.63

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