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- PDB-7rad: Crystal Structure Analysis of ALDH1B1 -

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Basic information

Entry
Database: PDB / ID: 7rad
TitleCrystal Structure Analysis of ALDH1B1
ComponentsAldehyde dehydrogenase X, mitochondrial
KeywordsOXIDOREDUCTASE / mitochondrial metabolism / pancreas cancer / colorectal cancer
Function / homology
Function and homology information


ethanol catabolic process / Ethanol oxidation / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix / mitochondrion ...ethanol catabolic process / Ethanol oxidation / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm / cytosol
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-ZGJ / Aldehyde dehydrogenase X, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsFernandez, D. / Chen, J.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127030 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM113100 United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Inhibitors targeted to aldehyde dehydrogenase
Authors: Fernandez, D.
History
DepositionJul 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Aldehyde dehydrogenase X, mitochondrial
B: Aldehyde dehydrogenase X, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,09016
Polymers109,4282
Non-polymers2,66214
Water1,71195
1
A: Aldehyde dehydrogenase X, mitochondrial
B: Aldehyde dehydrogenase X, mitochondrial
hetero molecules

A: Aldehyde dehydrogenase X, mitochondrial
B: Aldehyde dehydrogenase X, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,18132
Polymers218,8564
Non-polymers5,32528
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area29240 Å2
ΔGint-111 kcal/mol
Surface area56460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.127, 101.127, 185.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-738-

HOH

21B-729-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aldehyde dehydrogenase X, mitochondrial / Aldehyde dehydrogenase 5 / Aldehyde dehydrogenase family 1 member B1


Mass: 54714.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1B1, ALDH5, ALDHX / Production host: Escherichia coli (E. coli) / References: UniProt: P30837, aldehyde dehydrogenase (NAD+)

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Non-polymers , 5 types, 109 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ZGJ / 3-(2-methoxyphenyl)-1-(4-phenylphenyl)-6,7,8,9-tetrahydro-5~{H}-imidazo[1,2-a][1,3]diazepine


Mass: 396.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H26N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, Glycerol, ethyleneglycol, bicine/tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2021 / Details: Flat side-deflecting, Rh-coated Si mirrors
RadiationMonochromator: Liquid nitrogen-cooled double-crystal Si(111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→87.579 Å / Num. obs: 48771 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rpim(I) all: 0.06 / Rrim(I) all: 0.172 / Rsym value: 0.16 / Net I/av σ(I): 2.5 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.311-2.4281.0890.770130.4091.1661.089100
2.42-2.577.60.769166710.2960.8260.769100
2.57-2.758.70.5261.462570.190.560.526100
2.75-2.978.50.3472.158610.1270.3710.347100
2.97-3.258.20.218354060.0820.2340.218100
3.25-3.647.50.1573.848950.0630.170.15799.7
3.64-4.28.60.1284.243510.0470.1370.128100
4.2-5.148.60.1234.337070.0460.1310.123100
5.14-7.277.60.1194.329120.0470.1290.11999.5
7.27-46.388.10.1174.516980.0440.1260.11799.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3n80

3n80


Resolution: 2.3→30.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.171 / SU ML: 0.213 / SU R Cruickshank DPI: 0.3435 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 2484 5.1 %RANDOM
Rwork0.1973 ---
obs0.2005 46140 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.54 Å2 / Biso mean: 56.079 Å2 / Biso min: 31.94 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20.71 Å2-0 Å2
2--1.41 Å20 Å2
3----4.58 Å2
Refinement stepCycle: final / Resolution: 2.3→30.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7638 0 182 95 7915
Biso mean--59 53.6 -
Num. residues----986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198000
X-RAY DIFFRACTIONr_bond_other_d0.0020.027512
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.97710853
X-RAY DIFFRACTIONr_angle_other_deg0.962317253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1724.286364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.938151275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7751548
X-RAY DIFFRACTIONr_chiral_restr0.0930.21173
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021868
LS refinement shellResolution: 2.311→2.371 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 185 -
Rwork0.302 3286 -
all-3471 -
obs--98.22 %

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