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- PDB-8tcu: Structure of PYCR1 complexed with 2-chloro-5-(2-oxoimidazolidin-1... -

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Basic information

Entry
Database: PDB / ID: 8tcu
TitleStructure of PYCR1 complexed with 2-chloro-5-(2-oxoimidazolidin-1-yl)benzoic 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 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)169,34615
Polymers167,6635
Non-polymers1,68410
Water7,152397
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)338,69330
Polymers335,32610
Non-polymers3,36720
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area63710 Å2
ΔGint-715 kcal/mol
Surface area85140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.009, 178.914, 88.078
Angle α, β, γ (deg.)90.00, 107.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

21A-574-

HOH

31E-507-

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-ZR3 / 2-chloro-5-(2-oxoimidazolidin-1-yl)benzoic acid


Mass: 240.643 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H9ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 350 mM Li2SO4, 20% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM 2-chloro-5-(2-oxoimidazolidin-1-yl)benzoic acid. Crystal was soaked in ...Details: Reservoir contained 350 mM Li2SO4, 20% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM 2-chloro-5-(2-oxoimidazolidin-1-yl)benzoic acid. Crystal was soaked in cryobuffer containing 0 mM Li2SO4, 20% PEG 200, and 25 mM 2-chloro-5-(2-oxoimidazolidin-1-yl)benzoic 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→89.46 Å / Num. obs: 103502 / % possible obs: 95.6 % / Redundancy: 2.2 % / CC1/2: 0.983 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.106 / Rrim(I) all: 0.166 / Χ2: 1.34 / Net I/σ(I): 9.4 / Num. measured all: 232533
Reflection shellResolution: 2→2.03 Å / % possible obs: 95.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.768 / Num. measured all: 11044 / Num. unique obs: 5121 / CC1/2: 0.412 / Rpim(I) all: 0.638 / Rrim(I) all: 1.003 / Χ2: 0.99 / Net I/σ(I) obs: 1.3

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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→89.46 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 5204 5.03 %
Rwork0.189 --
obs0.1905 103471 95.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→89.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9868 0 105 397 10370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710165
X-RAY DIFFRACTIONf_angle_d0.88913825
X-RAY DIFFRACTIONf_dihedral_angle_d12.9163540
X-RAY DIFFRACTIONf_chiral_restr0.0491676
X-RAY DIFFRACTIONf_plane_restr0.0081780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.31791590.28683229X-RAY DIFFRACTION94
2.02-2.050.3151570.2763352X-RAY DIFFRACTION97
2.05-2.070.28971720.26343329X-RAY DIFFRACTION97
2.07-2.10.29671720.25053354X-RAY DIFFRACTION97
2.1-2.130.26571960.24913230X-RAY DIFFRACTION97
2.13-2.150.27291610.23963350X-RAY DIFFRACTION98
2.15-2.190.26791690.233365X-RAY DIFFRACTION97
2.19-2.220.27871870.22313298X-RAY DIFFRACTION97
2.22-2.250.24591750.22133319X-RAY DIFFRACTION97
2.25-2.290.24561740.21313301X-RAY DIFFRACTION97
2.29-2.330.24321630.21423398X-RAY DIFFRACTION97
2.33-2.370.29571940.21793289X-RAY DIFFRACTION96
2.37-2.420.26251570.21583255X-RAY DIFFRACTION96
2.42-2.470.2651650.2113318X-RAY DIFFRACTION97
2.47-2.520.2481560.1993323X-RAY DIFFRACTION96
2.52-2.580.23591660.19673237X-RAY DIFFRACTION95
2.58-2.640.24931700.20253206X-RAY DIFFRACTION94
2.64-2.710.2141830.20113204X-RAY DIFFRACTION94
2.71-2.790.27161630.19813184X-RAY DIFFRACTION92
2.79-2.880.24211530.20042980X-RAY DIFFRACTION87
2.88-2.990.23811830.19313328X-RAY DIFFRACTION97
2.99-3.110.21421700.19453371X-RAY DIFFRACTION98
3.11-3.250.22151930.20233291X-RAY DIFFRACTION97
3.25-3.420.21531920.19033324X-RAY DIFFRACTION97
3.42-3.630.21121850.17863308X-RAY DIFFRACTION96
3.63-3.910.18391990.15893271X-RAY DIFFRACTION96
3.91-4.310.18981900.14793265X-RAY DIFFRACTION96
4.31-4.930.15891750.13813213X-RAY DIFFRACTION93
4.93-6.210.21081660.18233054X-RAY DIFFRACTION88
6.21-89.460.16171590.16193321X-RAY DIFFRACTION95
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)
10.49580.07490.56260.2278-0.16382.21610.0395-0.09740.0080.0724-0.0201-0.02970.01120.1282-0.02450.1992-0.0018-0.02020.2382-0.01230.282826.0672173.627624.616
21.28550.4276-1.26120.4187-0.36312.38580.1139-0.05410.0588-0.0817-0.0223-0.1077-0.25170.349-0.08560.2208-0.013-0.0010.2389-0.02380.289832.6587183.0279-5.8274
30.4625-0.0597-0.22641.0245-0.60382.4318-0.0764-0.1537-0.09050.19390.01630.03670.47520.01350.06580.38170.03890.00480.2190.00220.278110.1095139.345918.8052
41.0755-0.4284-0.92740.77550.25392.3088-0.02890.0017-0.074-0.15240.0047-0.13560.26450.47290.02790.29050.0692-0.00370.2713-0.01010.287426.231145.1423-7.906
50.62190.0898-0.52461.1870.61022.58520.1455-0.20760.17360.1974-0.04620.0437-0.35820.1568-0.0840.2493-0.03670.02140.2378-0.02630.307-0.1092200.780216.104
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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