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- PDB-7mer: Structure of ALDH4A1 complexed with trans-4-Hydroxy-L-proline -

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Basic information

Entry
Database: PDB / ID: 7mer
TitleStructure of ALDH4A1 complexed with trans-4-Hydroxy-L-proline
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / Rossmann fold / nucleotide binding / acting on aldehyde or oxo group of donors / NAD or NADP as acceptor / mitochondria
Function / homology
Function and homology information


Proline catabolism / Glyoxylate metabolism and glycine degradation / 1-pyrroline-5-carboxylate dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / proline catabolic process to glutamate / aldehyde dehydrogenase (NAD+) 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
4-HYDROXYPROLINE / DI(HYDROXYETHYL)ETHER / Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.74 Å
AuthorsBogner, A.N. / Stiers, K.M. / Tanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132640 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Structural basis for the stereospecific inhibition of the dual proline/hydroxyproline catabolic enzyme ALDH4A1 by trans-4-hydroxy-L-proline.
Authors: Bogner, A.N. / Stiers, K.M. / McKay, C.M. / Becker, D.F. / Tanner, J.J.
History
DepositionApr 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9459
Polymers123,9082
Non-polymers1,0377
Water13,637757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-43 kcal/mol
Surface area34450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.056, 94.600, 132.587
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 61954.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aldh4a1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8CHT0, L-glutamate gamma-semialdehyde dehydrogenase

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Non-polymers , 5 types, 764 molecules

#2: Chemical ChemComp-HYP / 4-HYDROXYPROLINE / HYDROXYPROLINE / Hydroxyproline


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis Tris pH 6-7, 15-25% PEG 3350, and 0.2 M Li2SO4
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.74→132.59 Å / Num. obs: 110402 / % possible obs: 99.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 16.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.048 / Rrim(I) all: 0.139 / Net I/σ(I): 11.9 / Num. measured all: 904402 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.74-1.777.21.0783759152070.6620.4181.161.995.6
9.51-132.597.40.03257297740.9990.0120.03432.798.5

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3V9J

3v9j


Resolution: 1.74→77.01 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1896 5538 5.02 %
Rwork0.1639 104770 -
obs0.1652 110308 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.31 Å2 / Biso mean: 17.6193 Å2 / Biso min: 7.35 Å2
Refinement stepCycle: final / Resolution: 1.74→77.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8173 0 67 757 8997
Biso mean--26.52 24 -
Num. residues----1067
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.760.36681730.33583217339093
1.76-1.780.31241700.278734593629100
1.78-1.80.26262040.249934653669100
1.8-1.820.29341930.240434713664100
1.82-1.850.24561680.21834693637100
1.85-1.870.26091820.192834703652100
1.87-1.90.19061630.181435093672100
1.9-1.930.20341730.169534713644100
1.93-1.960.19591770.161434603637100
1.96-1.990.17451830.162234593642100
1.99-2.020.22492020.160634573659100
2.02-2.060.21950.162934673662100
2.06-2.10.19911790.16334783657100
2.1-2.140.20631850.170834823667100
2.14-2.190.21091800.176635013681100
2.19-2.240.22321700.177535013671100
2.24-2.30.18252010.16634693670100
2.3-2.360.16841790.154335003679100
2.36-2.430.20041730.159134733646100
2.43-2.510.21211750.160635223697100
2.51-2.590.2031860.159534963682100
2.59-2.70.18261770.1635103687100
2.7-2.820.18641990.162734963695100
2.82-2.970.18542020.157235133715100
2.97-3.160.18031920.164935153707100
3.16-3.40.19581840.167535363720100
3.4-3.740.16681890.143835313720100
3.74-4.280.14311900.13435623752100
4.28-5.40.14631890.13173581377099
5.4-77.010.16652050.15763730393599
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)
10.4497-0.012-0.02110.2460.09570.5057-0.0041-0.01990.0365-0.01360.0083-0.0095-0.03490.025-0.01350.0954-0.00040.00330.06770.00740.100819.9010.65163.4589
20.7785-0.143-0.15230.32910.06690.2446-0.0184-0.16650.06380.0550.02420.0017-0.02420.0072-0.00080.13220.0101-0.00350.1071-0.01190.1107-12.63346.947518.9385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and peptide and (not resname HYP)A0
2X-RAY DIFFRACTION2chain B and peptide and (not resname HYP)B0

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