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- PDB-8td1: Structure of PYCR1 complexed with 3-(6-Oxa-9-azaspiro(4.5)decane-... -

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Basic information

Entry
Database: PDB / ID: 8td1
TitleStructure of PYCR1 complexed with 3-(6-Oxa-9-azaspiro(4.5)decane-9-carbonyl)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
DI(HYDROXYETHYL)ETHER / : / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.88 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)169,60015
Polymers167,6635
Non-polymers1,93710
Water7,656425
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)339,20030
Polymers335,32610
Non-polymers3,87420
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area63790 Å2
ΔGint-635 kcal/mol
Surface area85850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.677, 180.247, 87.584
Angle α, β, γ (deg.)90.00, 106.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

21A-570-

HOH

31E-510-

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-ZRZ / 3-(6-oxa-9-azaspiro[4.5]decane-9-carbonyl)benzoic acid


Mass: 289.326 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H19NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 400 mM Li2SO4, 19% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM 3-(6-Oxa-9-azaspiro[4.5]decane-9-carbonyl)benzoic acid. Crystal was soaked ...Details: Reservoir contained 400 mM Li2SO4, 19% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM 3-(6-Oxa-9-azaspiro[4.5]decane-9-carbonyl)benzoic acid. Crystal was soaked in cryobuffer containing 0 mM Li2SO4, 20% PEG 200, and 25 mM 3-(6-Oxa-9-azaspiro[4.5]decane-9-carbonyl)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: 1.88→91.41 Å / Num. obs: 131474 / % possible obs: 98.8 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.04 / Rrim(I) all: 0.087 / Net I/σ(I): 12.1 / Num. measured all: 602723
Reflection shellResolution: 1.88→1.91 Å / % possible obs: 98.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 1.896 / Num. measured all: 28771 / Num. unique obs: 6533 / CC1/2: 0.254 / Rpim(I) all: 0.994 / Rrim(I) all: 2.152 / 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: 1.88→91.41 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 6490 4.95 %
Rwork0.1819 --
obs0.183 131203 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→91.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9908 0 132 425 10465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710231
X-RAY DIFFRACTIONf_angle_d0.9213921
X-RAY DIFFRACTIONf_dihedral_angle_d14.8783595
X-RAY DIFFRACTIONf_chiral_restr0.0511684
X-RAY DIFFRACTIONf_plane_restr0.0081792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90.36592030.34724051X-RAY DIFFRACTION96
1.9-1.920.33812100.32764138X-RAY DIFFRACTION97
1.92-1.950.31692180.30244114X-RAY DIFFRACTION98
1.95-1.970.32832060.29524158X-RAY DIFFRACTION99
1.97-20.31112190.27524148X-RAY DIFFRACTION99
2-2.020.28842140.26054162X-RAY DIFFRACTION99
2.02-2.050.27052130.25294073X-RAY DIFFRACTION97
2.05-2.080.27252060.23844111X-RAY DIFFRACTION97
2.08-2.120.25822280.22244191X-RAY DIFFRACTION100
2.12-2.150.2742330.22284167X-RAY DIFFRACTION100
2.15-2.190.2272300.21334206X-RAY DIFFRACTION100
2.19-2.230.25172250.20574176X-RAY DIFFRACTION100
2.23-2.270.22352110.18974168X-RAY DIFFRACTION100
2.27-2.320.21882490.18094158X-RAY DIFFRACTION99
2.32-2.370.23292230.17684202X-RAY DIFFRACTION100
2.37-2.420.21542050.18534169X-RAY DIFFRACTION99
2.42-2.480.19451920.17634228X-RAY DIFFRACTION99
2.48-2.550.22012240.17134167X-RAY DIFFRACTION99
2.55-2.630.20552240.18474168X-RAY DIFFRACTION99
2.63-2.710.2232190.18244167X-RAY DIFFRACTION99
2.71-2.810.23012120.20084147X-RAY DIFFRACTION99
2.81-2.920.25992170.22354112X-RAY DIFFRACTION97
2.92-3.050.22182040.20524070X-RAY DIFFRACTION97
3.05-3.210.21412470.18644163X-RAY DIFFRACTION99
3.21-3.420.22412090.18944222X-RAY DIFFRACTION99
3.42-3.680.20722100.17744211X-RAY DIFFRACTION99
3.68-4.050.15671960.15354189X-RAY DIFFRACTION99
4.05-4.640.16562110.13464198X-RAY DIFFRACTION99
4.64-5.840.17941950.16334089X-RAY DIFFRACTION96
5.84-91.410.14662370.15144190X-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)
10.64450.12060.46530.3744-0.0072.31450.0789-0.1657-0.0080.1374-0.0312-0.03460.14670.1807-0.04870.2460.0119-0.02640.3144-0.02910.293726.6487174.040924.335
20.8210.2284-0.80050.3217-0.17871.79750.0716-0.06280.0381-0.0497-0.0186-0.0934-0.20240.3618-0.04360.2693-0.0164-0.01060.3571-0.03370.33232.9359183.2624-5.9191
30.5317-0.144-0.27861.0124-0.50991.9817-0.0982-0.1583-0.13080.15510.00120.01870.37120.03040.11420.42710.0541-0.00530.29190.01050.338810.368139.461718.7134
41.0579-0.3586-0.81810.70370.11412.0008-0.03430.0071-0.1007-0.1652-0.0314-0.14990.3250.45150.0790.40380.115-0.01020.3388-0.00630.35126.3616144.8613-7.9706
50.4721-0.0502-0.41680.87910.49362.02170.0536-0.17350.11620.13850.00130.0105-0.22410.1436-0.05180.2861-0.02050.01020.2882-0.01760.37810.1545201.016415.9657
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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