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- PDB-8tcz: Structure of PYCR1 complexed with 2-(pyridin-2-yl)cyclopropane-1-... -

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Basic information

Entry
Database: PDB / ID: 8tcz
TitleStructure of PYCR1 complexed with 2-(pyridin-2-yl)cyclopropane-1-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: 2.1 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)168,40212
Polymers167,6635
Non-polymers7407
Water5,116284
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)336,80524
Polymers335,32610
Non-polymers1,47914
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area59500 Å2
ΔGint-715 kcal/mol
Surface area87630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.147, 179.293, 87.865
Angle α, β, γ (deg.)90.00, 106.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

21A-431-

HOH

31E-405-

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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZRI / (1S,2S)-2-(pyridin-2-yl)cyclopropane-1-carboxylic acid


Mass: 163.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 450 mM Li2SO4, 17.5% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM 2-(pyridin-2-yl)cyclopropane-1-carboxylic acid. Crystal was soaked in ...Details: Reservoir contained 450 mM Li2SO4, 17.5% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM 2-(pyridin-2-yl)cyclopropane-1-carboxylic acid. Crystal was soaked in cryobuffer containing 0 mM Li2SO4, 20% PEG 200, and 125 mM 2-(pyridin-2-yl)cyclopropane-1-carboxylic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→90.89 Å / Num. obs: 93857 / % possible obs: 99.2 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.042 / Rrim(I) all: 0.094 / Net I/σ(I): 11 / Num. measured all: 444668
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 97.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.994 / Num. measured all: 19742 / Num. unique obs: 4547 / CC1/2: 0.47 / Rpim(I) all: 0.532 / Rrim(I) all: 1.134 / Net I/σ(I) obs: 1.4

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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: 2.1→84.11 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 4597 4.9 %
Rwork0.1782 --
obs0.1796 93810 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→84.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9783 0 42 284 10109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810008
X-RAY DIFFRACTIONf_angle_d0.89513632
X-RAY DIFFRACTIONf_dihedral_angle_d12.9493461
X-RAY DIFFRACTIONf_chiral_restr0.0491677
X-RAY DIFFRACTIONf_plane_restr0.0081761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.27041630.26572868X-RAY DIFFRACTION98
2.12-2.150.27831660.26082883X-RAY DIFFRACTION96
2.15-2.180.30771510.25032908X-RAY DIFFRACTION98
2.18-2.20.25071710.23473003X-RAY DIFFRACTION100
2.2-2.230.29471610.23032951X-RAY DIFFRACTION100
2.23-2.260.26781660.22193006X-RAY DIFFRACTION100
2.26-2.290.26131660.2132990X-RAY DIFFRACTION100
2.29-2.330.27141570.20652981X-RAY DIFFRACTION100
2.33-2.370.22831540.21032965X-RAY DIFFRACTION100
2.37-2.40.22411640.19482989X-RAY DIFFRACTION100
2.4-2.450.24481560.23040X-RAY DIFFRACTION100
2.45-2.490.26381460.18862953X-RAY DIFFRACTION100
2.49-2.540.23841430.18442988X-RAY DIFFRACTION100
2.54-2.590.20711530.18312990X-RAY DIFFRACTION100
2.59-2.650.26351360.19943003X-RAY DIFFRACTION100
2.65-2.710.24721420.19862998X-RAY DIFFRACTION100
2.71-2.780.22921420.20952995X-RAY DIFFRACTION100
2.78-2.850.21741560.20562980X-RAY DIFFRACTION99
2.85-2.930.22881700.20782952X-RAY DIFFRACTION98
2.93-3.030.24191500.19962895X-RAY DIFFRACTION97
3.03-3.140.20981430.18822875X-RAY DIFFRACTION96
3.14-3.260.20661440.19413024X-RAY DIFFRACTION100
3.26-3.410.23961350.19963026X-RAY DIFFRACTION100
3.41-3.590.2191550.18712991X-RAY DIFFRACTION100
3.59-3.820.18081660.16262991X-RAY DIFFRACTION100
3.82-4.110.16981470.15232987X-RAY DIFFRACTION100
4.11-4.520.15541530.13963012X-RAY DIFFRACTION100
4.52-5.180.15131490.14082988X-RAY DIFFRACTION99
5.18-6.530.23071470.18612935X-RAY DIFFRACTION97
6.53-84.110.15221450.13863046X-RAY DIFFRACTION99
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)
10.45710.06550.66580.2053-0.06922.46490.0273-0.12250.0080.0893-0.0155-0.04270.07430.0397-0.00750.2247-0.0036-0.03230.3119-0.01690.350226.5031174.027524.5663
21.5770.5566-1.35060.4738-0.45682.34930.0625-0.01960.0454-0.0935-0.0076-0.1255-0.21790.2683-0.06040.3006-0.011-0.01780.3347-0.02950.393133.0142183.2781-5.8124
30.5219-0.1277-0.34781.3723-0.70882.8573-0.1081-0.1531-0.12690.2856-0.04440.06850.422-0.01470.1550.44420.02780.02030.294-0.01520.378310.4804139.502519.0068
41.4907-0.7531-1.37181.16410.53763.22130.02790.0232-0.0544-0.2201-0.0066-0.19260.16870.5813-0.01750.35770.0557-0.02180.3834-0.01020.382926.2849145.0876-7.6027
50.77980.2292-0.52831.47520.55142.94260.1411-0.28030.14740.279-0.12610.092-0.42760.1634-0.02580.3508-0.0436-0.0040.335-0.01170.39380.0024201.042515.8522
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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