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- PDB-8td0: Structure of PYCR1 complexed with 5-oxo-7a-phenyl-hexahydropyrrol... -

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Basic information

Entry
Database: PDB / ID: 8td0
TitleStructure of PYCR1 complexed with 5-oxo-7a-phenyl-hexahydropyrrolo[2,1-b][1,3]thiazole-3-carboxylic acid
ComponentsPyrroline-5-carboxylate reductase 1, mitochondrial
KeywordsOXIDOREDUCTASE / AMINO-ACID BIOSYNTHESIS / PROLINE BIOSYNTHESIS
Function / homology
Function and homology information


pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / Glutamate and glutamine metabolism / proline biosynthetic process / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrial membrane potential / cellular response to oxidative stress / mitochondrial matrix / mitochondrion / identical protein binding
Similarity search - Function
: / Delta 1-pyrroline-5-carboxylate reductase signature. / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsTanner, J.J. / Meeks, K.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132640 United States
CitationJournal: J.Chem.Inf.Model. / Year: 2024
Title: Novel Fragment Inhibitors of PYCR1 from Docking-Guided X-ray Crystallography.
Authors: Meeks, K.R. / Ji, J. / Protopopov, M.V. / Tarkhanova, O.O. / Moroz, Y.S. / Tanner, J.J.
History
DepositionJul 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,57411
Polymers167,6635
Non-polymers9116
Water1,78399
1
A: Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules

A: Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,14722
Polymers335,32610
Non-polymers1,82212
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area59700 Å2
ΔGint-642 kcal/mol
Surface area88020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.349, 179.119, 87.914
Angle α, β, γ (deg.)90.00, 106.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

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Components

#1: Protein
Pyrroline-5-carboxylate reductase 1, mitochondrial / P5C reductase 1 / P5CR 1


Mass: 33532.574 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PYCR1 / Production host: Escherichia coli (E. coli)
References: UniProt: P32322, pyrroline-5-carboxylate reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZS5 / (3R,4S,7aR)-5-oxo-7a-phenylhexahydropyrrolo[2,1-b][1,3]thiazole-3-carboxylic acid


Mass: 263.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 450 mM Li2SO4, 19% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM 5-oxo-7a-phenyl-hexahydropyrrolo[2,1-b][1,3]thiazole-3-carboxylic acid. ...Details: Reservoir contained 450 mM Li2SO4, 19% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM 5-oxo-7a-phenyl-hexahydropyrrolo[2,1-b][1,3]thiazole-3-carboxylic acid. Crystal was soaked in cryobuffer containing 0 mM Li2SO4, 20% PEG 200, and 25 mM 5-oxo-7a-phenyl-hexahydropyrrolo[2,1-b][1,3]thiazole-3-carboxylic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→90.37 Å / Num. obs: 80789 / % possible obs: 99 % / Redundancy: 4.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.101 / Rrim(I) all: 0.215 / Net I/σ(I): 6.9 / Num. measured all: 373849
Reflection shellResolution: 2.2→2.24 Å / % possible obs: 99.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 1.721 / Num. measured all: 21086 / Num. unique obs: 4437 / CC1/2: 0.463 / Rpim(I) all: 0.878 / Rrim(I) all: 1.937 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→90.37 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 30.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 3873 4.82 %
Rwork0.2218 --
obs0.2236 80335 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→90.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9706 0 56 99 9861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089917
X-RAY DIFFRACTIONf_angle_d1.05813512
X-RAY DIFFRACTIONf_dihedral_angle_d12.7153380
X-RAY DIFFRACTIONf_chiral_restr0.0541651
X-RAY DIFFRACTIONf_plane_restr0.0091756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.36371220.38292614X-RAY DIFFRACTION94
2.23-2.260.44371320.36212708X-RAY DIFFRACTION97
2.26-2.290.381620.35982688X-RAY DIFFRACTION98
2.29-2.320.41821450.3462696X-RAY DIFFRACTION98
2.32-2.350.34751390.33682707X-RAY DIFFRACTION99
2.35-2.390.36951360.3232809X-RAY DIFFRACTION99
2.39-2.420.34531390.32422711X-RAY DIFFRACTION99
2.42-2.460.37631450.31062733X-RAY DIFFRACTION99
2.46-2.50.33431270.29342788X-RAY DIFFRACTION99
2.5-2.550.36251510.28342736X-RAY DIFFRACTION99
2.55-2.60.32041500.28322731X-RAY DIFFRACTION99
2.6-2.650.29151430.27772747X-RAY DIFFRACTION99
2.65-2.710.29851270.26052773X-RAY DIFFRACTION99
2.71-2.770.31611390.25752732X-RAY DIFFRACTION99
2.77-2.840.30861220.26052762X-RAY DIFFRACTION98
2.84-2.920.31321350.2532714X-RAY DIFFRACTION98
2.92-3.010.29031410.27032682X-RAY DIFFRACTION97
3.01-3.10.32991460.25772629X-RAY DIFFRACTION96
3.1-3.210.28951380.23522762X-RAY DIFFRACTION99
3.21-3.340.26531340.23512768X-RAY DIFFRACTION99
3.34-3.490.25751500.21862755X-RAY DIFFRACTION99
3.49-3.680.24351580.21452695X-RAY DIFFRACTION99
3.68-3.910.25761390.19992766X-RAY DIFFRACTION99
3.91-4.210.22351310.18232770X-RAY DIFFRACTION99
4.21-4.630.18241340.16812738X-RAY DIFFRACTION98
4.63-5.30.22451240.18382751X-RAY DIFFRACTION98
5.3-6.680.23641370.20622706X-RAY DIFFRACTION96
6.68-90.370.16071270.15172791X-RAY DIFFRACTION98
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)
10.9282-0.06791.45070.2143-0.3474.10830.0301-0.27320.020.0781-0.0049-0.05010.10470.1239-0.00770.296-0.0143-0.05550.5888-0.02240.485826.1532173.794824.4638
22.82671.0498-2.67490.4616-0.58154.26870.130.1305-0.0146-0.102-0.0055-0.116-0.39250.2394-0.13260.3260.0379-0.03680.5042-0.02930.436232.7363183.2622-5.969
30.5751-0.4623-0.54271.2311-0.38845.4861-0.2102-0.2292-0.12610.2788-0.03150.07891.0719-0.01430.23740.55440.03670.01060.4511-0.02460.480910.2881139.833618.8498
41.4886-0.693-1.1021.20121.02333.20430.029-0.0315-0.0639-0.22380.0924-0.26890.12640.8835-0.08950.4020.0726-0.01740.64390.0120.48325.9967145.4267-7.7554
51.25120.1992-1.34661.64590.68473.66550.2786-0.48020.24690.2575-0.08690.0663-0.70420.4597-0.17110.4327-0.0859-0.01140.5528-0.01840.4927-0.1625200.862315.5441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1peptide and chain A
2X-RAY DIFFRACTION2peptide and chain B
3X-RAY DIFFRACTION3peptide and chain C
4X-RAY DIFFRACTION4peptide and chain D
5X-RAY DIFFRACTION5peptide and chain E

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