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- PDB-3v9k: Crystal structure of mouse 1-pyrroline-5-carboxylate dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 3v9k
TitleCrystal structure of mouse 1-pyrroline-5-carboxylate dehydrogenase complexed with the product glutamate
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 / 1-pyrroline-5-carboxylate dehydrogenase activity / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 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)124,3876
Polymers123,9082
Non-polymers4784
Water16,141896
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-30 kcal/mol
Surface area33760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.820, 93.954, 132.241
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 42.15 %
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: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 27, 2011
RadiationMonochromator: Rosenbaum-Rock Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.501→46.977 Å / Num. all: 168017 / Num. obs: 168017 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rsym value: 0.066 / Net I/σ(I): 25.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allRsym value% possible all
1.501-1.586.70.418159500237280.41897.4
1.58-1.687.30.305169275231270.305100
1.68-1.797.40.217159924217480.217100
1.79-1.947.40.137149531202730.137100
1.94-2.127.40.083138480186970.083100
2.12-2.377.40.058125849169420.058100
2.37-2.747.40.044111761150270.044100
2.74-3.367.40.03194826127780.031100
3.36-4.757.30.0227318199760.022100
4.75-46.9777.10.024037357210.0299.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V9J

3v9j


Resolution: 1.501→46.977 Å / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.9229 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1691 8509 5.07 %SAME TEST SET AS PDB ENTRY 3V9J
Rwork0.1513 ---
obs0.1523 167897 99.6 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.218 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 41.58 Å2 / Biso mean: 11.1311 Å2 / Biso min: 3.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.3483 Å20 Å2-0 Å2
2--1.8693 Å20 Å2
3----0.259 Å2
Refinement stepCycle: LAST / Resolution: 1.501→46.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8157 0 32 896 9085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068565
X-RAY DIFFRACTIONf_angle_d1.09111694
X-RAY DIFFRACTIONf_chiral_restr0.0711292
X-RAY DIFFRACTIONf_plane_restr0.0051538
X-RAY DIFFRACTIONf_dihedral_angle_d11.6723057
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.501-1.55480.21278250.1866151681599396
1.5548-1.61710.19178450.15751587316718100
1.6171-1.69070.17649190.15051582216741100
1.6907-1.77980.16438110.14211591916730100
1.7798-1.89130.17448090.14181594016749100
1.8913-2.03730.16588400.14131594616786100
2.0373-2.24240.16538190.14171600816827100
2.2424-2.56680.15758500.15011602416874100
2.5668-3.23380.16988920.15761612317015100
3.2338-470.16188990.15281656517464100

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