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- PDB-3v9g: Crystal structure of human 1-pyrroline-5-carboxylate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3v9g
TitleCrystal structure of human 1-pyrroline-5-carboxylate dehydrogenase
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 / proline metabolic process / trans-4-hydroxy-L-proline catabolic process / L-proline catabolic process / 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 / electron transfer activity ...Proline catabolism / proline metabolic process / trans-4-hydroxy-L-proline catabolic process / L-proline catabolic process / 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 / electron transfer 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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 1.2Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
C: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
D: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)248,0774
Polymers248,0774
Non-polymers00
Water00
1
A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)124,0382
Polymers124,0382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-30 kcal/mol
Surface area34540 Å2
MethodPISA
2
C: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
D: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)124,0382
Polymers124,0382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-30 kcal/mol
Surface area34050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.717, 150.717, 191.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 35 - 562 / Label seq-ID: 38 - 565

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 35:562)AA
2chain B and (resseq 35:562)BB
3chain C and (resseq 35:562)CC
4chain D and (resseq 35:562)DD

NCS oper:
IDCodeMatrixVector
1given(0.737825, 0.67466, -0.02119), (0.674629, -0.738094, -0.009664), (-0.022161, -0.007165, -0.999729)-32.6759, 90.122498, 179.835999
2given(-0.712684, -0.684883, -0.151711), (-0.644305, 0.553575, 0.52766), (-0.277402, 0.473804, -0.835798)132.535995, 7.31451, 146.136993
3given(-0.952182, -0.133579, 0.274785), (-0.015441, -0.877177, -0.479918), (0.305142, -0.461212, 0.833169)64.9319, 173.207993, 30.4214

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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: 62019.188 Da / Num. of mol.: 4 / Fragment: UNP residues 18-563
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH4, ALDH4A1, P5CDH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P30038, EC: 1.5.1.12

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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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: reservoir: 22.5% PEG3350, 0.2 M ammonium sulfate, 0.1 M HEPES, cryoprotectant: 25% PEG3350, 0.2 M ammonium sulfate, 0.1 M HEPES, 25% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979181 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979181 Å / Relative weight: 1
ReflectionRedundancy: 5.8 % / Av σ(I) over netI: 17.03 / Number: 661829 / Rmerge(I) obs: 0.1 / Χ2: 3.74 / D res high: 2.85 Å / D res low: 50 Å / Num. obs: 113595 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.145010010.0518.7865.8
4.876.1410010.0783.4415.8
4.264.8710010.0772.8215.8
3.874.2610010.0792.0855.8
3.593.8710010.0981.9045.8
3.383.5910010.1311.8395.8
3.213.3810010.1991.7025.8
3.073.2110010.291.635.8
2.953.0710010.3941.6385.8
2.852.9510010.5241.6885.8
ReflectionResolution: 2.5→50 Å / Num. obs: 84960 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.075 / Χ2: 1.566 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.593.80.53984981.4871100
2.59-2.693.80.39384781.5261100
2.69-2.823.80.28384851.5151100
2.82-2.963.80.18485041.5241100
2.96-3.153.80.1384981.5031100
3.15-3.393.80.08885111.4851100
3.39-3.733.80.06384811.3521100
3.73-4.273.80.05785561.495199.9
4.27-5.383.70.05985291.821199.7
5.38-503.70.05584201.982197.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXautosolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→38.665 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7801 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 2005 2.36 %RANDOM
Rwork0.2039 ---
obs0.2048 84851 99.68 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.72 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 151.62 Å2 / Biso mean: 63.5665 Å2 / Biso min: 16.65 Å2
Baniso -1Baniso -2Baniso -3
1-3.3239 Å2-0 Å2-0 Å2
2--3.3239 Å20 Å2
3----6.6478 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16032 0 0 0 16032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916458
X-RAY DIFFRACTIONf_angle_d1.22222493
X-RAY DIFFRACTIONf_chiral_restr0.0772530
X-RAY DIFFRACTIONf_plane_restr0.0052940
X-RAY DIFFRACTIONf_dihedral_angle_d13.625633
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3923X-RAY DIFFRACTIONPOSITIONAL0.076
12B3923X-RAY DIFFRACTIONPOSITIONAL0.076
13C3891X-RAY DIFFRACTIONPOSITIONAL0.073
14D3878X-RAY DIFFRACTIONPOSITIONAL0.071
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.58980.36721980.3057829384918293100
2.5898-2.69340.35232000.297826084608260100
2.6934-2.8160.3381980.2809828284808282100
2.816-2.96440.36031970.2686830485018304100
2.9644-3.150.3342020.2516828484868284100
3.15-3.39310.28282050.2411829685018296100
3.3931-3.73430.22771970.2102828384808283100
3.7343-4.27410.22232080.1745832785358327100
4.2741-5.38260.1782020.1545830585078305100
5.3826-38.66960.17731980.173482128410821298
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)
10.1568-0.0944-0.01590.1983-0.02150.223-0.05020.06-0.1106-0.1907-0.0028-0.048-0.19110.20.03610.18250.09760.00110.0660.09810.105517.620360.502471.6173
20.0267-0.03630.03770.0654-0.06650.1408-0.0869-0.2607-0.13210.0749-0.035-0.0258-0.06620.07360.01680.06340.2195-0.08690.1260.4867-0.222419.566656.5018107.3403
30.20480.0270.04380.5076-0.16680.3787-0.0004-0.05740.1010.10640.0825-0.129-0.2081-0.0210.01150.404-0.068-0.15110.21540.06810.327768.308772.7071107.7879
40.3716-0.04310.01820.6679-0.61520.5465-0.05880.29890.023-0.30160.0706-0.06040.19290.02180.02480.6898-0.1657-0.15270.41310.26960.408659.252686.318675.5131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA0
2X-RAY DIFFRACTION2chain BB0
3X-RAY DIFFRACTION3chain CC0
4X-RAY DIFFRACTION4chain DD0

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