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- PDB-4e3x: Crystal Structure of Mus musculus 1-pyrroline-5-carboxylate dehyd... -

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Basic information

Entry
Database: PDB / ID: 4e3x
TitleCrystal Structure of Mus musculus 1-pyrroline-5-carboxylate dehydrogenase cryoprotected in proline
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / Amino Acid Metabolism / Proline Inhibition
Function / homology
Function and homology information


Proline catabolism / Glyoxylate metabolism and glycine degradation / L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,6,9,12,15,18-HEXAOXAICOSANE / TRIETHYLENE GLYCOL / PROLINE / Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsTanner, J.J. / Pemberton, T.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Proline: Mother Nature's cryoprotectant applied to protein crystallography.
Authors: Pemberton, T.A. / Still, B.R. / Christensen, E.M. / Singh, H. / Srivastava, D. / Tanner, J.J.
History
DepositionMar 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 13, 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)125,15911
Polymers123,9082
Non-polymers1,2509
Water15,889882
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-32 kcal/mol
Surface area34620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.980, 93.878, 132.406
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aldh4a1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q8CHT0, EC: 1.5.1.12
#2: Chemical
ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-16P / 3,6,9,12,15,18-HEXAOXAICOSANE


Mass: 294.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O6
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 42.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 20% PEG 3350, 0.1 M Bis-Tris, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.24→45.639 Å / Num. all: 279378 / Num. obs: 279378 / % possible obs: 94.1 % / Redundancy: 4.1 % / Rsym value: 0.051 / Net I/σ(I): 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.24-1.313.30.551.4123860375610.5587.3
1.31-1.393.50.3472.2131970374290.34792
1.39-1.483.70.2133.6134218358280.21393.6
1.48-1.640.135.9134266337530.1394.5
1.6-1.754.30.0928.2135194314970.09295.8
1.75-1.964.60.06511.1131108287640.06596.2
1.96-2.274.70.04614.9119223255860.04696.9
2.27-2.774.80.03717.8104421219500.03797.8
2.77-3.924.90.03118.584937173570.03199
3.92-45.6394.60.03215.74485996530.03297.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3V9J

3v9j


Resolution: 1.24→40.4793 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9065 / SU ML: 0.18 / σ(F): 0 / Phase error: 16.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1803 14042 5.03 %
Rwork0.1549 --
obs0.1562 279273 93.9 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.375 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 42.41 Å2 / Biso mean: 12.6721 Å2 / Biso min: 4.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.9617 Å20 Å20 Å2
2--0.5154 Å2-0 Å2
3---0.4467 Å2
Refinement stepCycle: LAST / Resolution: 1.24→40.4793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8234 0 85 882 9201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058652
X-RAY DIFFRACTIONf_angle_d1.07811801
X-RAY DIFFRACTIONf_chiral_restr0.0731304
X-RAY DIFFRACTIONf_plane_restr0.0061544
X-RAY DIFFRACTIONf_dihedral_angle_d12.1063109
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 (%)
1.24-1.25510.4744090.43097322773178
1.2551-1.26990.42824340.38198392882689
1.2699-1.28540.39244790.35458340881990
1.2854-1.30170.34184390.29778420885990
1.3017-1.31880.3024160.26748535895191
1.3188-1.33680.27814310.23568545897691
1.3368-1.35590.27234320.2148595902792
1.3559-1.37620.23524250.18488636906192
1.3762-1.39770.23314850.178607909293
1.3977-1.42060.1944370.15518746918393
1.4206-1.44510.20374720.15048680915293
1.4451-1.47140.18374710.14068783925494
1.4714-1.49970.17384600.12718803926394
1.4997-1.53030.15644730.11958776924994
1.5303-1.56360.1514880.11568825931394
1.5636-1.59990.15674550.11718868932395
1.5999-1.640.15345050.11678895940095
1.64-1.68430.16295180.11578877939595
1.6843-1.73390.15044710.11839033950496
1.7339-1.78980.15514440.12059047949196
1.7898-1.85380.15634440.12539051949596
1.8538-1.9280.16854850.13119064954996
1.928-2.01580.16584770.13429107958497
2.0158-2.1220.15744740.13879102957697
2.122-2.2550.16644590.13319175963497
2.255-2.42910.15245030.13779192969597
2.4291-2.67350.15595150.15029277979298
2.6735-3.06020.17024990.16179412991199
3.0602-3.85510.16385250.15395051003099
3.8551-40.47930.17465170.165296211013897

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