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- PDB-4lh2: Structure of mouse 1-Pyrroline-5-Carboxylate Dehydrogenase (ALDH4... -

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Basic information

Entry
Database: PDB / ID: 4lh2
TitleStructure of mouse 1-Pyrroline-5-Carboxylate Dehydrogenase (ALDH4A1) complexed with succinate
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / Proline catabolism / Substrate recognition / Rossmann Fold
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; 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 ...Delta-1-pyrroline-5-carboxylate dehydrogenase / 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
SUCCINIC ACID / Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.673 Å
AuthorsPemberton, T.A. / Tanner, J.J.
CitationJournal: Arch.Biochem.Biophys. / Year: 2013
Title: Structural basis of substrate selectivity of Delta (1)-pyrroline-5-carboxylate dehydrogenase (ALDH4A1): Semialdehyde chain length.
Authors: Pemberton, T.A. / Tanner, J.J.
History
DepositionJun 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Sep 20, 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_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)124,6216
Polymers123,9082
Non-polymers7134
Water14,394799
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-26 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.884, 94.091, 132.339
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 61954.215 Da / Num. of mol.: 2 / Fragment: unp residues 21-562
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ADLH4a1, Aldh4a1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CHT0, EC: 1.5.1.12
#2: 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
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 799 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15-25% PEG 3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 148 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 24, 2012
RadiationMonochromator: osmic blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.673→19.677 Å / Num. all: 118798 / Num. obs: 118798 / % possible obs: 97 % / Redundancy: 4.6 % / Rsym value: 0.055 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.67-1.763.50.3422.254933155450.34287.9
1.76-1.874.20.2522.965802158390.25294.8
1.87-24.40.1564.767994153030.15697.4
2-2.164.80.1066.970666146880.10699.8
2.16-2.3750.0759.667564135790.07599.9
2.37-2.655.10.0581262826123150.05899.9
2.65-3.055.10.04614.355807108960.04699.9
3.05-3.745.20.039164776292720.03999.9
3.74-5.295.20.03317.93789372900.033100
5.29-19.67750.03216.72034140710.03298

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 4V9J

4v9j


Resolution: 1.673→19.677 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8904 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.04 / Phase error: 18.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 5928 5 %common set
Rwork0.1636 ---
obs0.1649 118798 95.04 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.816 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso max: 61.46 Å2 / Biso mean: 15.9034 Å2 / Biso min: 4.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.9079 Å2-0 Å2-0 Å2
2---0.621 Å20 Å2
3----0.2869 Å2
Refinement stepCycle: LAST / Resolution: 1.673→19.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8154 0 48 799 9001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068471
X-RAY DIFFRACTIONf_angle_d1.03211536
X-RAY DIFFRACTIONf_chiral_restr0.071272
X-RAY DIFFRACTIONf_plane_restr0.0051511
X-RAY DIFFRACTIONf_dihedral_angle_d11.9373028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6732-1.69220.31532480.2854536478460
1.6922-1.71210.27993250.2476097642282
1.7121-1.7330.23963420.21756618696088
1.733-1.75490.23013420.2046635697789
1.7549-1.7780.23043210.20336769709090
1.778-1.80230.23383400.19936754709490
1.8023-1.82810.21473290.20166839716891
1.8281-1.85530.26132990.21226828712790
1.8553-1.88430.23453970.19776837723492
1.8843-1.91520.21523480.17177028737694
1.9152-1.94810.19943840.1667063744795
1.9481-1.98350.19473600.16167207756796
1.9835-2.02170.19943810.16327310769198
2.0217-2.06290.18764170.16477403782099
2.0629-2.10770.21123670.16457448781599
2.1077-2.15670.22434020.159674337835100
2.1567-2.21050.19833890.154474547843100
2.2105-2.27020.16783510.152374907841100
2.2702-2.33690.18324260.156974217847100
2.3369-2.41220.20813780.155475217899100
2.4122-2.49830.19763870.159474867873100
2.4983-2.59810.17094080.155674247832100
2.5981-2.7160.18974510.164674097860100
2.716-2.85880.20023620.16875477909100
2.8588-3.03730.17244250.164474257850100
3.0373-3.27090.19364230.177574427865100
3.2709-3.59820.17594210.156274137834100
3.5982-4.11470.15774040.136174557859100
4.1147-5.16850.14233910.124474527843100
5.1685-19.6780.17213940.170174967890100
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)
10.225-0.0417-0.06310.08010.05620.1507-0.0039-0.02410.0285-0.00360.0229-0.0305-0.00630.0487-0.0180.0115-0.00180.00240.0886-0.00410.089119.60040.74693.4381
20.2579-0.0631-0.0350.09410.04260.1218-0.0218-0.05950.00520.0002-0.00310.021-0.0056-0.04450.02510.00050.01040.00190.0737-0.01150.0751-12.30867.071718.3914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA30 - 563
2X-RAY DIFFRACTION2Chain BB20 - 563

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