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

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Basic information

Entry
Database: PDB / ID: 7mjd
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 / 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-ZGG / Aldehyde dehydrogenase X, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 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
DepositionApr 20, 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)116,84028
Polymers110,2032
Non-polymers6,63726
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-68 kcal/mol
Surface area33400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.040, 102.040, 186.037
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-804-

HOH

21B-758-

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: 55101.434 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 , 6 types, 212 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-ZGG / 8-(2-methoxyphenyl)-10-(4-phenylphenyl)-1$l^{4},8-diazabicyclo[5.3.0]deca-1(7),9-diene


Mass: 395.516 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H27N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.49 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 4000, glycerol, tris-bicine, ethyleneglycols

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2018
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.12→88.369 Å / Num. all: 64238 / Num. obs: 64238 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Rsym value: 0.081 / Net I/av σ(I): 3.8 / Net I/σ(I): 11.4 / Num. measured all: 431121
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.12-2.236.90.79316392792640.3270.8590.7932.3100
2.23-2.376.80.5141.55963188020.2140.5580.5143.499.9
2.37-2.536.30.3422.25210282220.1480.3740.3424.699.8
2.53-2.7470.233.35390177280.0940.2490.236.9100
2.74-36.90.154.84890471390.0620.1630.159.8100
3-3.356.40.0924.24135864200.040.1010.09214.999.6
3.35-3.8770.0669.44013457430.0270.0720.06622.2100
3.87-4.746.50.05753167948760.0250.0630.05727.499.7
4.74-6.76.70.052112592338440.0210.0560.05226.999.9
6.7-37.2076.20.04611.11356222000.020.050.04627.898.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å12.36 Å
Translation2.5 Å12.36 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.6.1phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N80

3n80


Resolution: 2.12→30.37 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.3 / SU ML: 0.137 / SU R Cruickshank DPI: 0.2089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 3298 5.1 %RANDOM
Rwork0.1805 ---
obs0.1825 60846 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.71 Å2 / Biso mean: 48.122 Å2 / Biso min: 23.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å20 Å2
2--0.79 Å2-0 Å2
3----2.56 Å2
Refinement stepCycle: final / Resolution: 2.12→30.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7704 0 240 186 8130
Biso mean--49.37 51.46 -
Num. residues----986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198112
X-RAY DIFFRACTIONr_bond_other_d0.0060.027702
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.98110960
X-RAY DIFFRACTIONr_angle_other_deg0.965317712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6185984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51624.301372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.281151322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3351550
X-RAY DIFFRACTIONr_chiral_restr0.0960.21176
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219152
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021880
LS refinement shellResolution: 2.12→2.175 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 210 -
Rwork0.251 4458 -
all-4668 -
obs--99.68 %

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