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- PDB-8rkq: Structure of human DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE ... -

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Basic information

Entry
Database: PDB / ID: 8rkq
TitleStructure of human DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE (ALDH4A1) complexed with the molecular tweezer CLR01
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / ALDH4A1 / ROSSMANN FOLD / NAD / MOLECULAR TWEEZER / SUPRAMOLECULAR LIGANDS / PROTEIN-PROTEIN INTERACTIONS
Function / homology
Function and homology information


Proline catabolism / proline metabolic process / 4-hydroxyproline catabolic process / proline catabolic process / 1-pyrroline-5-carboxylate dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / proline catabolic process to glutamate / aldehyde dehydrogenase (NAD+) activity / Glyoxylate metabolism and glycine degradation / electron transfer activity ...Proline catabolism / proline metabolic process / 4-hydroxyproline catabolic process / proline catabolic process / 1-pyrroline-5-carboxylate dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / proline catabolic process to glutamate / aldehyde dehydrogenase (NAD+) activity / Glyoxylate metabolism and glycine degradation / electron transfer activity / mitochondrial matrix / mitochondrion / identical protein binding / cytosol
Similarity search - Function
Delta-1-pyrroline-5-carboxylate dehydrogenase / 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
Chem-9SZ / Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPorfetye, A.T. / Vetter, I.R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1093 Germany
CitationJournal: Molecules / Year: 2024
Title: How Do Molecular Tweezers Bind to Proteins? Lessons from X-ray Crystallography.
Authors: Porfetye, A.T. / Stege, P. / Rebollido-Rios, R. / Hoffmann, D. / Schrader, T. / Vetter, I.R.
History
DepositionDec 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
C: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
D: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,3285
Polymers248,6024
Non-polymers7271
Water99155
1
A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


  • defined by author&software
  • Evidence: equilibrium centrifugation, domain-swapped homodimer, see Srivastava D, Singh RK, Moxley MA, Henzl MT, Becker DF, Tanner JJ. The three-dimensional structural basis of type II ...Evidence: equilibrium centrifugation, domain-swapped homodimer, see Srivastava D, Singh RK, Moxley MA, Henzl MT, Becker DF, Tanner JJ. The three-dimensional structural basis of type II hyperprolinemia. J Mol Biol. 2012 Jul 13;420(3):176-89. doi: 10.1016/j.jmb.2012.04.010. Epub 2012 Apr 16. PMID: 22516612; PMCID: PMC3372638.
  • 125 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)125,0273
Polymers124,3012
Non-polymers7271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-30 kcal/mol
Surface area36720 Å2
MethodPISA
2
C: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
D: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial


  • defined by author&software
  • Evidence: equilibrium centrifugation, domain-swapped homodimer, see Srivastava D, Singh RK, Moxley MA, Henzl MT, Becker DF, Tanner JJ. The three-dimensional structural basis of type II ...Evidence: equilibrium centrifugation, domain-swapped homodimer, see Srivastava D, Singh RK, Moxley MA, Henzl MT, Becker DF, Tanner JJ. The three-dimensional structural basis of type II hyperprolinemia. J Mol Biol. 2012 Jul 13;420(3):176-89. doi: 10.1016/j.jmb.2012.04.010. Epub 2012 Apr 16. PMID: 22516612; PMCID: PMC3372638.
  • 124 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)124,3012
Polymers124,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-24 kcal/mol
Surface area36690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.752, 148.752, 189.957
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial / P5C dehydrogenase / Aldehyde dehydrogenase family 4 member A1 / L-glutamate gamma-semialdehyde dehydrogenase


Mass: 62150.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH4A1, ALDH4, P5CDH / Plasmid: pET28 / Production host: Escherichia coli (E. coli)
References: UniProt: P30038, L-glutamate gamma-semialdehyde dehydrogenase
#2: Chemical ChemComp-9SZ / (1R,5S,9S,16R,20R,24S,28S,35R)-3,22-Bis(dihydroxyphosphoryloxy)tridecacyclo[22.14.1.15,20.19,16.128,35.02,23.04,21.06,19.08,17.010,15.025,38.027,36.029,34]dotetraconta-2(23),3,6,8(17),10,12,14,18,21,25,27(36),29,31,33,37-pentadecaene


Mass: 726.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H32O8P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2M ammonium citrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97794 Å / Relative weight: 1
ReflectionResolution: 2.6→48.69 Å / Num. obs: 72820 / % possible obs: 99.5 % / Redundancy: 8.99 % / Biso Wilson estimate: 80.073 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.139 / Χ2: 0.923 / Net I/σ(I): 9.25 / Num. measured all: 654686
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.678.3212.2490.9743869539152720.6032.39797.8
2.67-2.749.3971.5941.4449072526252220.7621.68699.2
2.74-2.829.5611.2641.8448742512350980.831.33599.5
2.82-2.99.4870.8472.6446797496449330.9140.89699.4
2.9-39.3680.6413.4845012483048050.9350.67899.5
3-3.119.1740.5174.2542823468846680.9530.54899.6
3.11-3.228.6280.3815.4438602448844740.9680.40699.7
3.22-3.359.0030.3076.9238685432142970.980.32599.4
3.35-3.59.4980.2429.1139140414641210.9870.25699.4
3.5-3.679.3480.19811.3437309400139910.9890.2199.8
3.67-3.879.1470.16712.7534357376137560.9910.17799.9
3.87-4.118.6660.13914.7731026359335800.9920.14899.6
4.11-4.397.9960.11716.2226753335233460.9930.12599.8
4.39-4.748.90.10618.928054315331520.9950.113100
4.74-5.28.7660.119.5525124286828660.9950.10699.9
5.2-5.818.6770.09719.4122735262126200.9950.103100
5.81-6.718.010.08919.4218503231323100.9950.09599.9
6.71-8.229.0620.07522.2817779196319620.9960.0899.9
8.22-11.628.4710.06223.2512799151215110.9970.06699.9
11.62-48.698.9770.04824.0975058498360.9980.05198.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.69 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 23.987 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.447 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 2101 2.9 %RANDOM
Rwork0.2307 ---
obs0.232 70717 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 167.1 Å2 / Biso mean: 86.127 Å2 / Biso min: 47.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å21.15 Å20 Å2
2--2.29 Å2-0 Å2
3----7.44 Å2
Refinement stepCycle: final / Resolution: 2.6→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16829 0 52 55 16936
Biso mean--102.35 70.24 -
Num. residues----2176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01317322
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715957
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.64623525
X-RAY DIFFRACTIONr_angle_other_deg1.0991.57837084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74152172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46622.399838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.649152811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2881592
X-RAY DIFFRACTIONr_chiral_restr0.0460.22222
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0219478
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023670
X-RAY DIFFRACTIONr_mcbond_it1.3949.2798700
X-RAY DIFFRACTIONr_mcbond_other1.3949.2788699
X-RAY DIFFRACTIONr_mcangle_it2.40813.91810868
LS refinement shellResolution: 2.6→2.665 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.417 152 -
Rwork0.413 5110 -
obs--97.75 %

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