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- PDB-4wj9: Structure of Human apo ALDH1A1 -

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Basic information

Entry
Database: PDB / ID: 4wj9
TitleStructure of Human apo ALDH1A1
ComponentsRetinal dehydrogenase 1
KeywordsOXIDOREDUCTASE / Oxidoreductase Aldehyde dehydrogenase
Function / homology
Function and homology information


fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Fructose catabolism ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Fructose catabolism / Ethanol oxidation / cellular aldehyde metabolic process / RA biosynthesis pathway / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / androgen binding / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / negative regulation of cold-induced thermogenesis / retinol metabolic process / retinoid metabolic process / GTPase activator activity / NAD binding / axon / synapse / extracellular exosome / cytoplasm / cytosol
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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...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
YTTERBIUM (III) ION / Aldehyde dehydrogenase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.74 Å
AuthorsMorgan, C.A. / Hurley, T.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)R01AA018123 United States
CitationJournal: Chem.Biol.Interact. / Year: 2015
Title: Development of a high-throughput in vitro assay to identify selective inhibitors for human ALDH1A1.
Authors: Morgan, C.A. / Hurley, T.D.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinal dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1063
Polymers54,8981
Non-polymers2082
Water4,432246
1
A: Retinal dehydrogenase 1
hetero molecules

A: Retinal dehydrogenase 1
hetero molecules

A: Retinal dehydrogenase 1
hetero molecules

A: Retinal dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,42412
Polymers219,5904
Non-polymers8348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_555x,-y,-z1
Buried area21600 Å2
ΔGint-134 kcal/mol
Surface area60470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.297, 109.297, 83.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
SymmetryPoint symmetry: (Schoenflies symbol: C (n fold cyclic))

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Components

#1: Protein Retinal dehydrogenase 1 / RalDH1 / ALDH-E1 / ALHDII / Aldehyde dehydrogenase family 1 member A1 / Aldehyde dehydrogenase / cytosolic


Mass: 54897.590 Da / Num. of mol.: 1 / Mutation: N121S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A1, ALDC, ALDH1, PUMB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00352, retinal dehydrogenase
#2: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Yb
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 300 K / Method: evaporation / pH: 7
Details: PEG3350, sodium chloride, 100 mM Bis Tris Buffer, ytterbium chloride, sitting drop
PH range: 6.2-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.74→109.3 Å / Num. obs: 48862 / % possible obs: 99 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 31.5
Reflection shellHighest resolution: 1.74 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.9 / % possible all: 97

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 1.74→109.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.184 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21562 2631 5.1 %RANDOM
Rwork0.18472 ---
obs0.1863 48862 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.122 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0 Å20 Å2
2---0.58 Å20 Å2
3---1.16 Å2
Refinement stepCycle: 1 / Resolution: 1.74→109.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 2 246 4038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193936
X-RAY DIFFRACTIONr_bond_other_d0.0010.023765
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9625327
X-RAY DIFFRACTIONr_angle_other_deg0.73238703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5345503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85424.699166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89815678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5191517
X-RAY DIFFRACTIONr_chiral_restr0.0710.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02871
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_it0.6771.5231990
X-RAY DIFFRACTIONr_mcbond_other0.661.5221988
X-RAY DIFFRACTIONr_mcangle_it1.082.2812490
X-RAY DIFFRACTIONr_mcangle_other1.0832.2812491
X-RAY DIFFRACTIONr_scbond_it1.51.6781946
X-RAY DIFFRACTIONr_scbond_other1.0341.6721938
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6642.4522833
X-RAY DIFFRACTIONr_long_range_B_refined4.99913.0844553
X-RAY DIFFRACTIONr_long_range_B_other4.94712.7194477
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.744→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 171 -
Rwork0.256 3427 -
obs--95.03 %
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)
13.708-0.08970.01390.8635-0.6841.5819-0.1588-0.381-0.59610.3002-0.00190.13080.18650.05460.16080.31020.08280.22950.13560.18810.321851.254-33.335727.2727
21.09430.0124-0.26961.0462-0.14410.4476-0.2126-0.2291-0.35070.21730.03610.05420.06670.0160.17650.12870.04870.10220.09080.08140.150556.5545-19.685315.5918
33.310.06590.2650.54030.07120.4554-0.155-0.5457-0.0160.29920.04550.13120.0137-0.03030.10940.20580.07220.07840.18130.05260.067349.3989-7.386626.9528
45.5094-0.92442.53422.3123-0.82639.6724-0.118-0.2354-0.1257-0.00990.23380.32620.4313-0.2688-0.11580.0622-0.00990.06450.04420.03470.194222.8176-13.430712.8308
52.0526-0.2857-0.09752.5174-0.87060.9149-0.2088-0.3546-0.30190.35640.1250.43060.0138-0.11570.08380.21910.06670.24910.21870.08680.300625.0653-16.233226.9374
61.65360.2404-0.1521.5657-0.27190.9551-0.1887-0.19350.02270.16490.1310.3421-0.0176-0.03140.05760.09740.04410.06110.08460.00650.111633.585-1.668714.3365
71.61740.8494-1.02923.0768-1.62941.7855-0.0408-0.02510.17870.15450.10990.0704-0.0713-0.015-0.06910.0433-0.0026-0.02870.03080.01540.042669.76853.9075.0272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 49
2X-RAY DIFFRACTION2A50 - 224
3X-RAY DIFFRACTION3A225 - 282
4X-RAY DIFFRACTION4A283 - 295
5X-RAY DIFFRACTION5A296 - 408
6X-RAY DIFFRACTION6A409 - 483
7X-RAY DIFFRACTION7A484 - 501

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