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- PDB-4qgk: Structure of the Human Sjogren Larsson Syndrome enzyme fatty alde... -

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Basic information

Entry
Database: PDB / ID: 4qgk
TitleStructure of the Human Sjogren Larsson Syndrome enzyme fatty aldehyde dehydrogenase (FALDH)
ComponentsFatty aldehyde dehydrogenaseLong-chain-aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde dehydrogenase / Fatty aldehyde dehydrogenase / Sjogren Larsson Syndrome
Function / homology
Function and homology information


farnesal dehydrogenase / sesquiterpenoid metabolic process / hexadecanal metabolic process / long-chain-alcohol oxidase activity / long-chain-aldehyde dehydrogenase activity / medium-chain-aldehyde dehydrogenase activity / phytol metabolic process / Alpha-oxidation of phytanate / 3-chloroallyl aldehyde dehydrogenase activity / fatty acid alpha-oxidation ...farnesal dehydrogenase / sesquiterpenoid metabolic process / hexadecanal metabolic process / long-chain-alcohol oxidase activity / long-chain-aldehyde dehydrogenase activity / medium-chain-aldehyde dehydrogenase activity / phytol metabolic process / Alpha-oxidation of phytanate / 3-chloroallyl aldehyde dehydrogenase activity / fatty acid alpha-oxidation / Class I peroxisomal membrane protein import / cellular aldehyde metabolic process / : / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / peripheral nervous system development / aldehyde dehydrogenase (NAD+) activity / peroxisomal membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / epidermis development / central nervous system development / peroxisome / membrane => GO:0016020 / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity
Similarity search - Function
Aldehyde dehydrogenase NAD(P)-dependent / 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 NAD(P)-dependent / 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
Aldehyde dehydrogenase family 3 member A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZander, U. / Keller, M. / Marquez, J.A.
CitationJournal: Nat Commun / Year: 2014
Title: A gatekeeper helix determines the substrate specificity of Sjogren-Larsson Syndrome enzyme fatty aldehyde dehydrogenase.
Authors: Keller, M.A. / Zander, U. / Fuchs, J.E. / Kreutz, C. / Watschinger, K. / Mueller, T. / Golderer, G. / Liedl, K.R. / Ralser, M. / Krautler, B. / Werner, E.R. / Marquez, J.A.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Experimental preparation / Category: citation / exptl_crystal_grow
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.2Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty aldehyde dehydrogenase
B: Fatty aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)104,4732
Polymers104,4732
Non-polymers00
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-43 kcal/mol
Surface area34290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.137, 98.582, 145.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.33826, -0.532194, -0.776112), (-0.527156, -0.790341, 0.312197), (-0.779543, 0.303529, -0.54789)-1.5706, 4.2208, -5.67932

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Components

#1: Protein Fatty aldehyde dehydrogenase / Long-chain-aldehyde dehydrogenase / Aldehyde dehydrogenase 10 / Aldehyde dehydrogenase family 3 member A2 / Microsomal aldehyde dehydrogenase


Mass: 52236.348 Da / Num. of mol.: 2 / Fragment: Cytoplasmic domain, UNP residues 1-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH10, ALDH3A2, FALDH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P51648, aldehyde dehydrogenase (NAD+)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 9.5
Details: 0.2M Li2SO4, 0.1M CHES pH9.5, 1.0M K/Na Tartrate, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.97625
SYNCHROTRONESRF ID14-420.976
Detector
TypeIDDetector
DECTRIS PILATUS 6M-F1PIXEL
ADSC QUANTUM 42CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1channel cut cryogenically cooled monochromator crystalSINGLE WAVELENGTHMx-ray1
2Double Crystal Si(111)Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.976251
20.9761
ReflectionResolution: 2.1→30 Å / Num. all: 66310 / Num. obs: 66111 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SZA

3sza


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.431 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22257 3355 5.1 %RANDOM
Rwork0.1984 ---
all0.19962 66111 --
obs0.19962 62756 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.877 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å2-0 Å20 Å2
2---0.4 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7314 0 0 320 7634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0197503
X-RAY DIFFRACTIONr_bond_other_d0.0060.027377
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.97210161
X-RAY DIFFRACTIONr_angle_other_deg0.916316997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2465925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00124.307332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.607151366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3011545
X-RAY DIFFRACTIONr_chiral_restr0.1150.21148
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218389
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021672
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.433.9213694
X-RAY DIFFRACTIONr_mcbond_other3.4273.9213693
X-RAY DIFFRACTIONr_mcangle_it4.3215.8714621
X-RAY DIFFRACTIONr_mcangle_other4.3215.8724622
X-RAY DIFFRACTIONr_scbond_it5.7344.6243809
X-RAY DIFFRACTIONr_scbond_other5.7344.6253810
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.4316.6525541
X-RAY DIFFRACTIONr_long_range_B_refined9.64932.4898784
X-RAY DIFFRACTIONr_long_range_B_other9.65832.3978709
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 261 -
Rwork0.242 4668 -
obs--99.72 %

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