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- PDB-3v9j: Crystal structure of mouse 1-pyrroline-5-carboxylate dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 3v9j
TitleCrystal structure of mouse 1-pyrroline-5-carboxylate dehydrogenase complexed with sulfate ion
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 / 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
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.299 Å
AuthorsTanner, J.J. / Srivastava, D.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Three-Dimensional Structural Basis of Type II Hyperprolinemia.
Authors: Srivastava, D. / Singh, R.K. / Moxley, M.A. / Henzl, M.T. / Becker, D.F. / Tanner, J.J.
History
DepositionDec 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 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)124,66910
Polymers123,9082
Non-polymers7618
Water18,6461035
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-123 kcal/mol
Surface area34360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.228, 94.039, 132.390
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 / 1-pyrroline-5-carboxylate dehydrogenase / 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: Aldh4a1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8CHT0, EC: 1.5.1.12
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1035 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: reservoir: 20-25% w/v PEG3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5, cryoprotectant: 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.299→50 Å / Num. obs: 247337 / % possible obs: 94.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.055 / Χ2: 1.597 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.299-1.323.60.502111070.866186
1.32-1.353.70.437112770.868187.4
1.35-1.373.60.374113690.881188.3
1.37-1.43.60.323115590.868189.1
1.4-1.433.50.282116160.864189.9
1.43-1.463.40.235117790.888190.9
1.46-1.53.40.195119380.926192.2
1.5-1.543.30.167121370.952193.7
1.54-1.593.30.138123060.993195
1.59-1.643.30.122125001.073196.2
1.64-1.73.40.108125711.12197
1.7-1.763.40.093127051.239197.9
1.76-1.843.50.081128181.368198.4
1.84-1.943.60.073128471.683198.8
1.94-2.063.70.07129182.206199.1
2.06-2.223.80.067130092.772199.5
2.22-2.4540.061130722.862199.7
2.45-2.84.20.048131122.487199.7
2.8-3.534.60.038132212.584199.7
3.53-504.60.03134762.166198.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V9G

3v9g


Resolution: 1.299→29.42 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9257 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 13.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1596 12422 5.02 %RANDOM
Rwork0.1319 ---
obs0.1333 247235 94.88 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.853 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 48.05 Å2 / Biso mean: 13.2263 Å2 / Biso min: 4.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.159 Å20 Å2-0 Å2
2--0.568 Å20 Å2
3----0.6544 Å2
Refinement stepCycle: LAST / Resolution: 1.299→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8262 0 42 1035 9339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058668
X-RAY DIFFRACTIONf_angle_d1.05411835
X-RAY DIFFRACTIONf_chiral_restr0.0691302
X-RAY DIFFRACTIONf_plane_restr0.0061551
X-RAY DIFFRACTIONf_dihedral_angle_d12.0093093
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 (%)
1.299-1.31410.27793520.23346961731385
1.3141-1.32950.25423530.20757217757088
1.3295-1.34570.24233780.18857114749287
1.3457-1.36280.21343610.16567214757588
1.3628-1.38070.20083590.16117291765089
1.3807-1.39960.20024180.14897279769789
1.3996-1.41960.19713710.13327367773890
1.4196-1.44080.17323950.12197384777990
1.4408-1.46330.17313850.127463784891
1.4633-1.48730.17214070.117550795792
1.4873-1.51290.14924150.10447592800793
1.5129-1.54050.14434120.10167714812694
1.5405-1.57010.15164370.09967731816895
1.5701-1.60210.14734020.09737846824896
1.6021-1.6370.14714400.09297946838696
1.637-1.6750.13984550.0967888834397
1.675-1.71690.14334210.09688031845298
1.7169-1.76330.14624250.09728048847398
1.7633-1.81520.13414010.10318156855798
1.8152-1.87380.15033960.10558108850499
1.8738-1.94080.14794420.11438142858499
1.9408-2.01840.14544330.11558169860299
2.0184-2.11030.14224320.12298203863599
2.1103-2.22150.15514170.126982688685100
2.2215-2.36060.13744400.12482578697100
2.3606-2.54280.15934370.138183098746100
2.5428-2.79850.17114630.149582668729100
2.7985-3.2030.16114550.151683158770100
3.203-4.03390.15274640.143284268890100
4.0339-29.42710.16624560.15788558901498

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