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- PDB-3v9i: Crystal structure of human 1-pyrroline-5-carboxylate dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 3v9i
TitleCrystal structure of human 1-pyrroline-5-carboxylate dehydrogenase mutant S352L
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 / 4-hydroxyproline catabolic process / proline catabolic process / 1-pyrroline-5-carboxylate dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / proline catabolic process to glutamate / aldehyde dehydrogenase (NAD+) activity / Glyoxylate metabolism and glycine degradation / electron transfer activity ...Proline catabolism / proline metabolic process / 4-hydroxyproline catabolic process / proline catabolic process / 1-pyrroline-5-carboxylate dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / proline catabolic process to glutamate / aldehyde dehydrogenase (NAD+) activity / Glyoxylate metabolism and glycine degradation / 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, N-terminal / Aldehyde dehydrogenase, C-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 / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsTanner, J.J. / Singh, R.K.
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)248,1814
Polymers248,1814
Non-polymers00
Water0
1
A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)124,0912
Polymers124,0912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-28 kcal/mol
Surface area36580 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)124,0912
Polymers124,0912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-19 kcal/mol
Surface area38610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.382, 150.382, 192.518
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:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTHRTHRchain A and (resseq 30:41 or resseq 43:99 or resseq...AA30 - 4133 - 44
12GLYGLYLYSLYSchain A and (resseq 30:41 or resseq 43:99 or resseq...AA43 - 9946 - 102
13LEULEUALAALAchain A and (resseq 30:41 or resseq 43:99 or resseq...AA101 - 164104 - 167
14LEULEUVALVALchain A and (resseq 30:41 or resseq 43:99 or resseq...AA166 - 178169 - 181
15LEULEUGLYGLYchain A and (resseq 30:41 or resseq 43:99 or resseq...AA180 - 182183 - 185
16THRTHRTYRTYRchain A and (resseq 30:41 or resseq 43:99 or resseq...AA192 - 246195 - 249
17ILEILECYSCYSchain A and (resseq 30:41 or resseq 43:99 or resseq...AA248 - 315251 - 318
18GLYGLYGLYGLYchain A and (resseq 30:41 or resseq 43:99 or resseq...AA317320
19PHEPHEGLNGLNchain A and (resseq 30:41 or resseq 43:99 or resseq...AA320 - 346323 - 349
110TYRTYRALAALAchain A and (resseq 30:41 or resseq 43:99 or resseq...AA355 - 381358 - 384
111ASPASPLYSLYSchain A and (resseq 30:41 or resseq 43:99 or resseq...AA383 - 402386 - 405
112SERSERPROPROchain A and (resseq 30:41 or resseq 43:99 or resseq...AA409 - 442412 - 445
113ILEILESERSERchain A and (resseq 30:41 or resseq 43:99 or resseq...AA448 - 475451 - 478
114GLYGLYTHRTHRchain A and (resseq 30:41 or resseq 43:99 or resseq...AA477 - 511480 - 514
21LEULEUTHRTHRchain B and (resseq 30:41 or resseq 43:99 or resseq...BB30 - 4133 - 44
22GLYGLYLYSLYSchain B and (resseq 30:41 or resseq 43:99 or resseq...BB43 - 9946 - 102
23LEULEUALAALAchain B and (resseq 30:41 or resseq 43:99 or resseq...BB101 - 164104 - 167
24LEULEUVALVALchain B and (resseq 30:41 or resseq 43:99 or resseq...BB166 - 178169 - 181
25LEULEUGLYGLYchain B and (resseq 30:41 or resseq 43:99 or resseq...BB180 - 182183 - 185
26THRTHRTYRTYRchain B and (resseq 30:41 or resseq 43:99 or resseq...BB192 - 246195 - 249
27ILEILECYSCYSchain B and (resseq 30:41 or resseq 43:99 or resseq...BB248 - 315251 - 318
28GLYGLYGLYGLYchain B and (resseq 30:41 or resseq 43:99 or resseq...BB317320
29PHEPHEGLNGLNchain B and (resseq 30:41 or resseq 43:99 or resseq...BB320 - 346323 - 349
210TYRTYRALAALAchain B and (resseq 30:41 or resseq 43:99 or resseq...BB355 - 381358 - 384
211ASPASPLYSLYSchain B and (resseq 30:41 or resseq 43:99 or resseq...BB383 - 402386 - 405
212SERSERPROPROchain B and (resseq 30:41 or resseq 43:99 or resseq...BB409 - 439412 - 442
213ILEILESERSERchain B and (resseq 30:41 or resseq 43:99 or resseq...BB448 - 475451 - 478
214GLYGLYTHRTHRchain B and (resseq 30:41 or resseq 43:99 or resseq...BB477 - 511480 - 514
31LEULEUTHRTHRchain C and (resseq 30:41 or resseq 43:99 or resseq...CC30 - 4133 - 44
32GLYGLYLYSLYSchain C and (resseq 30:41 or resseq 43:99 or resseq...CC43 - 9946 - 102
33LEULEUALAALAchain C and (resseq 30:41 or resseq 43:99 or resseq...CC101 - 164104 - 167
34LEULEUVALVALchain C and (resseq 30:41 or resseq 43:99 or resseq...CC166 - 178169 - 181
35LEULEUGLYGLYchain C and (resseq 30:41 or resseq 43:99 or resseq...CC180 - 182183 - 185
36THRTHRTYRTYRchain C and (resseq 30:41 or resseq 43:99 or resseq...CC192 - 246195 - 249
37ILEILETRPTRPchain C and (resseq 30:41 or resseq 43:99 or resseq...CC248 - 295251 - 298
38GLNGLNCYSCYSchain C and (resseq 30:41 or resseq 43:99 or resseq...CC297 - 315300 - 318
39GLYGLYGLYGLYchain C and (resseq 30:41 or resseq 43:99 or resseq...CC317320
310PHEPHEGLNGLNchain C and (resseq 30:41 or resseq 43:99 or resseq...CC320 - 346323 - 349
311TYRTYRALAALAchain C and (resseq 30:41 or resseq 43:99 or resseq...CC355 - 381358 - 384
312ASPASPLYSLYSchain C and (resseq 30:41 or resseq 43:99 or resseq...CC383 - 402386 - 405
313SERSERSERSERchain C and (resseq 30:41 or resseq 43:99 or resseq...CC409 - 412412 - 415
314THRTHRGLUGLUchain C and (resseq 30:41 or resseq 43:99 or resseq...CC414 - 441417 - 444
315ILEILESERSERchain C and (resseq 30:41 or resseq 43:99 or resseq...CC448 - 475451 - 478
316LEULEUTHRTHRchain C and (resseq 30:41 or resseq 43:99 or resseq...CC478 - 511481 - 514
41LEULEUTHRTHRchain D and (resseq 30:41 or resseq 43:57 or resseq...DD30 - 4133 - 44
42GLYGLYLEULEUchain D and (resseq 30:41 or resseq 43:57 or resseq...DD43 - 5746 - 60
43GLYGLYGLYGLYchain D and (resseq 30:41 or resseq 43:57 or resseq...DD59 - 8862 - 91
44VALVALLYSLYSchain D and (resseq 30:41 or resseq 43:57 or resseq...DD91 - 9994 - 102
45LEULEUALAALAchain D and (resseq 30:41 or resseq 43:57 or resseq...DD102 - 164105 - 167
46LEULEUVALVALchain D and (resseq 30:41 or resseq 43:57 or resseq...DD166 - 178169 - 181
47LEULEUGLYGLYchain D and (resseq 30:41 or resseq 43:57 or resseq...DD180 - 182183 - 185
48THRTHRTYRTYRchain D and (resseq 30:41 or resseq 43:57 or resseq...DD192 - 246195 - 249
49ILEILECYSCYSchain D and (resseq 30:41 or resseq 43:57 or resseq...DD248 - 315251 - 318
410GLYGLYGLYGLYchain D and (resseq 30:41 or resseq 43:57 or resseq...DD317320
411PHEPHEGLNGLNchain D and (resseq 30:41 or resseq 43:57 or resseq...DD320 - 346323 - 349
412TYRTYRVALVALchain D and (resseq 30:41 or resseq 43:57 or resseq...DD355 - 356358 - 359
413HISHISHISHISchain D and (resseq 30:41 or resseq 43:57 or resseq...DD358 - 372361 - 375
414ARGARGVALVALchain D and (resseq 30:41 or resseq 43:57 or resseq...DD374 - 377377 - 380
415PHEPHEARGARGchain D and (resseq 30:41 or resseq 43:57 or resseq...DD387 - 399390 - 402
416LYSLYSLYSLYSchain D and (resseq 30:41 or resseq 43:57 or resseq...DD402405
417SERSERSERSERchain D and (resseq 30:41 or resseq 43:57 or resseq...DD409 - 424412 - 427
418TYRTYRGLNGLNchain D and (resseq 30:41 or resseq 43:57 or resseq...DD427 - 440430 - 443
419ILEILESERSERchain D and (resseq 30:41 or resseq 43:57 or resseq...DD448 - 475451 - 478
420GLYGLYTHRTHRchain D and (resseq 30:41 or resseq 43:57 or resseq...DD477 - 511480 - 514

NCS oper:
IDCodeMatrixVector
1given(0.730852, 0.682223, -0.020671), (0.68215, -0.731122, -0.01149), (-0.022952, -0.005703, -0.99972)-32.813, 89.495499, 180.102005
2given(-0.709288, -0.681042, -0.181915), (-0.659364, 0.549712, 0.51289), (-0.249299, 0.483735, -0.838958)135.438995, 10.1013, 144.813995
3given(-0.959486, -0.133748, 0.247987), (-0.005592, -0.870937, -0.491363), (0.2817, -0.472843, 0.834904)68.794899, 173.113007, 32.130699

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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: 62045.266 Da / Num. of mol.: 4 / Fragment: UNP residues 18-563 / Mutation: S352L
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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: reservoir: 22.5% PEG3350, 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 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: Nov 16, 2011
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: 2.839→47.784 Å / Num. all: 55880 / Num. obs: 55880 / % possible obs: 97.5 % / Redundancy: 3.2 % / Rsym value: 0.101 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.839-33.10.6262.22573782640.62699
3-3.193.20.4213.12474478350.42198.9
3.19-3.413.20.2594.72340773590.25998.7
3.41-3.683.20.1547.32166167990.15498.3
3.68-4.033.20.1059.91987262340.10598
4.03-4.513.20.075131782455920.07597
4.51-5.23.20.05915.21545749050.05996.2
5.2-6.373.10.0613.61287441100.0695.6
6.37-9.013.30.04217.31031431220.04293.8
9.01-47.693.30.03622.3546116600.03690.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCdata collection
XDSdata reduction
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V9G

3v9g


Resolution: 2.85→43.826 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8012 / SU ML: 0.9 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1338 2.4 %SAME TEST SET AS PDB ENTRY 3V9G
Rwork0.2093 ---
obs0.2106 55850 97.19 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.048 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 173.19 Å2 / Biso mean: 56.3441 Å2 / Biso min: 16.46 Å2
Baniso -1Baniso -2Baniso -3
1-10.6677 Å20 Å2-0 Å2
2--10.6677 Å20 Å2
3----1.0063 Å2
Refinement stepCycle: LAST / Resolution: 2.85→43.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13924 0 0 0 13924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114254
X-RAY DIFFRACTIONf_angle_d1.23119520
X-RAY DIFFRACTIONf_chiral_restr0.0792280
X-RAY DIFFRACTIONf_plane_restr0.0052537
X-RAY DIFFRACTIONf_dihedral_angle_d13.8894556
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3148X-RAY DIFFRACTIONPOSITIONAL0.086
12B3148X-RAY DIFFRACTIONPOSITIONAL0.086
13C3117X-RAY DIFFRACTIONPOSITIONAL0.069
14D2723X-RAY DIFFRACTIONPOSITIONAL0.095
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 (%)
2.85-2.95180.37721360.305955125648551299
2.9518-3.070.35061380.265355135651551399
3.07-3.20970.35591340.234755565690555699
3.2097-3.37880.27961370.227555025639550299
3.3788-3.59040.26351340.20555045638550498
3.5904-3.86750.25021370.198754795616547998
3.8675-4.25640.26571320.184454605592546097
4.2564-4.87170.2131350.169753925527539296
4.8717-6.13510.24071280.221253625490536295
6.1351-43.83140.25361270.208852325359523292

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