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- PDB-8tcw: Structure of PYCR1 complexed with 2-methyl-3-(2-oxoimidazolidin-1... -

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Basic information

Entry
Database: PDB / ID: 8tcw
TitleStructure of PYCR1 complexed with 2-methyl-3-(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 / : / 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: 1.94 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)169,34016
Polymers167,6635
Non-polymers1,67811
Water8,377465
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)338,68132
Polymers335,32610
Non-polymers3,35522
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area63920 Å2
ΔGint-733 kcal/mol
Surface area86560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.013, 178.781, 87.724
Angle α, β, γ (deg.)90.00, 106.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

21A-578-

HOH

31E-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-ZR6 / 2-methyl-3-(2-oxoimidazolidin-1-yl)benzoic acid


Mass: 220.225 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 350 mM Li2SO4, 18% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM 2-methyl-3-(2-oxoimidazolidin-1-yl)benzoic acid. Crystal was soaked in ...Details: Reservoir contained 350 mM Li2SO4, 18% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM 2-methyl-3-(2-oxoimidazolidin-1-yl)benzoic acid. Crystal was soaked in cryobuffer containing 0 mM Li2SO4, 20% PEG 200, and 125 mM 2-methyl-3-(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-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: 1.94→90.78 Å / Num. obs: 117909 / % possible obs: 98.9 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.044 / Rrim(I) all: 0.096 / Net I/σ(I): 11 / Num. measured all: 553724
Reflection shellResolution: 1.94→1.97 Å / % possible obs: 98.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.901 / Num. measured all: 25739 / Num. unique obs: 5797 / CC1/2: 0.696 / Rpim(I) all: 0.474 / Rrim(I) all: 1.022 / Net I/σ(I) obs: 1.5

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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: 1.94→61.22 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 5844 4.96 %
Rwork0.173 --
obs0.1741 117828 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→61.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10001 0 110 465 10576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710297
X-RAY DIFFRACTIONf_angle_d0.8513998
X-RAY DIFFRACTIONf_dihedral_angle_d12.8223601
X-RAY DIFFRACTIONf_chiral_restr0.0491687
X-RAY DIFFRACTIONf_plane_restr0.0081805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.960.29481740.28383689X-RAY DIFFRACTION98
1.96-1.990.29561900.26723715X-RAY DIFFRACTION98
1.99-2.010.2912030.25213603X-RAY DIFFRACTION96
2.01-2.040.26561970.2383752X-RAY DIFFRACTION99
2.04-2.060.2611790.2353752X-RAY DIFFRACTION99
2.06-2.090.24391870.20923780X-RAY DIFFRACTION99
2.09-2.120.24892070.20463717X-RAY DIFFRACTION100
2.12-2.150.25481990.20023772X-RAY DIFFRACTION100
2.15-2.190.21941840.19063749X-RAY DIFFRACTION99
2.19-2.220.22011850.18053737X-RAY DIFFRACTION99
2.22-2.260.21541890.18913781X-RAY DIFFRACTION99
2.26-2.30.211930.18123735X-RAY DIFFRACTION99
2.3-2.350.22151930.18173734X-RAY DIFFRACTION99
2.35-2.390.20611930.18593756X-RAY DIFFRACTION99
2.39-2.450.23312200.18573751X-RAY DIFFRACTION99
2.45-2.50.21011860.1813752X-RAY DIFFRACTION99
2.5-2.560.20461950.1713742X-RAY DIFFRACTION99
2.56-2.630.2121860.17883732X-RAY DIFFRACTION99
2.63-2.710.18922030.17343729X-RAY DIFFRACTION99
2.71-2.80.21392070.1873663X-RAY DIFFRACTION97
2.8-2.90.23591900.20183573X-RAY DIFFRACTION94
2.9-3.020.26062110.20073738X-RAY DIFFRACTION99
3.02-3.150.21041990.18333755X-RAY DIFFRACTION99
3.15-3.320.18781850.18213779X-RAY DIFFRACTION100
3.32-3.530.21072120.18113752X-RAY DIFFRACTION100
3.53-3.80.16092040.15843766X-RAY DIFFRACTION99
3.8-4.180.1612160.14523742X-RAY DIFFRACTION99
4.18-4.790.13911800.12923772X-RAY DIFFRACTION99
4.79-6.030.19311840.16653631X-RAY DIFFRACTION95
6.03-61.220.14241930.13783835X-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)
10.45280.08220.47570.2178-0.02372.12370.0354-0.10860.00280.088-0.0207-0.05460.07690.1056-0.01360.2296-0.0001-0.03510.2884-0.00830.297226.3679173.849724.6433
21.09920.3469-1.0410.2854-0.34821.95520.0744-0.02750.0357-0.0479-0.036-0.0967-0.21240.2318-0.04220.2657-0.0074-0.02290.2874-0.01490.310832.8889183.3178-5.9554
30.3934-0.0722-0.39420.8855-0.60452.5878-0.0775-0.1089-0.11420.1731-0.01850.01650.40850.00230.09990.36280.0209-0.01850.2402-0.00320.294510.2249139.41718.9849
41.1462-0.4671-1.25850.72870.37392.7302-0.0346-0.0231-0.0965-0.15160.02-0.13740.21250.47440.01530.31430.0493-0.01510.3101-0.01340.314126.354145.1103-8.0311
50.51850.0044-0.56420.97170.71832.59770.0812-0.2360.12640.1414-0.02050.0411-0.29270.1812-0.06470.2703-0.0216-0.0080.289-0.01960.3233-0.003200.907716.1288
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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