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- PDB-6xoz: Structure of human PYCR1 complexed with L-tetrahydro-2-furoic acid -

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Basic information

Entry
Database: PDB / ID: 6xoz
TitleStructure of human PYCR1 complexed with L-tetrahydro-2-furoic 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
ProC C-terminal domain-like / ProC C-terminal domain-like fold / : / 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 ...ProC C-terminal domain-like / ProC C-terminal domain-like fold / : / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAHYDROFURAN-2-CARBOXYLIC ACID / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsTanner, J.J. / Christensen, E.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM065546 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: In crystallo screening for proline analog inhibitors of the proline cycle enzyme PYCR1.
Authors: Christensen, E.M. / Bogner, A.N. / Vandekeere, A. / Tam, G.S. / Patel, S.M. / Becker, D.F. / Fendt, S.M. / Tanner, J.J.
History
DepositionJul 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 13, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)170,83211
Polymers170,2165
Non-polymers6166
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)341,66422
Polymers340,43210
Non-polymers1,23212
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area58100 Å2
ΔGint-545 kcal/mol
Surface area87570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.028, 120.170, 87.868
Angle α, β, γ (deg.)90.000, 108.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34043.156 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-TFB / TETRAHYDROFURAN-2-CARBOXYLIC ACID


Mass: 116.115 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Crystallization reservoir contained 3 M NaCl and 0.1 M HEPES at pH 7.5-8.0. Crystal was soaked in cryobuffer containing 50 mM L-tetrahydro-2-furoic acid and 30% glycerol.
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→60.085 Å / Num. obs: 72417 / % possible obs: 96.3 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.051 / Rrim(I) all: 0.096 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.43.10.5791092234940.7160.3790.694275.2
11.51-60.083.60.02224356680.9990.0130.02543.597.4

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5UAX

5uax


Resolution: 2.35→60.085 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 3593 4.97 %
Rwork0.1768 68686 -
obs0.1792 72279 96.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.74 Å2 / Biso mean: 46.4378 Å2 / Biso min: 14.82 Å2
Refinement stepCycle: final / Resolution: 2.35→60.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9814 0 41 284 10139
Biso mean--42.28 36.72 -
Num. residues----1373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.35-2.38090.34970.2445201173
2.3809-2.41360.33551150.2411216579
2.4136-2.4480.28221120.2334240386
2.448-2.48460.27241480.2263256295
2.4846-2.52340.2881480.2188270499
2.5234-2.56480.26241240.2147277599
2.5648-2.6090.26891720.2217267799
2.609-2.65650.29641470.2475269699
2.6565-2.70750.31231380.2402262197
2.7075-2.76280.3011300.2377272999
2.7628-2.82290.24461290.1981272699
2.8229-2.88860.25941450.196269999
2.8886-2.96080.25481320.2015272699
2.9608-3.04080.24651340.2115275699
3.0408-3.13030.26751350.2003271799
3.1303-3.23130.27171190.1975277899
3.2313-3.34680.27051520.1974270899
3.3468-3.48080.27471190.1746256994
3.4808-3.63920.20031420.1717275599
3.6392-3.8310.19491260.1567262995
3.831-4.0710.20951330.1553259994
4.071-4.38530.17681560.1311272899
4.3853-4.82640.1841540.1193270899
4.8264-5.52440.16821620.1405272899
5.5244-6.95850.20481690.17332737100
6.9585-60.0850.16111550.1453278098
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)
10.95510.5913-0.61091.1771-0.88092.22050.03390.16660.111-0.09890.0243-0.0583-0.21030.2311-0.050.2077-0.01220.02530.2744-0.0280.26819.8984163.4471-8.7899
20.64980.0990.16160.79710.17543.25670.0468-0.23050.12810.23620.0489-0.0516-0.14680.3182-0.08550.2183-0.01910.01280.2765-0.06960.280616.4512156.258622.3496
32.0386-0.3128-0.77180.6543-0.14661.38580.10940.078-0.0241-0.2092-0.0859-0.20850.15670.3837-0.01770.37710.15130.00250.3585-0.01440.30836.3998127.7693-2.8726
40.649-0.13130.07980.942-0.93382.6463-0.0149-0.2712-0.1490.0755-0.0248-0.03950.28860.10760.04580.31210.0912-0.01660.33150.020.30222.732118.935924.6281
50.8964-0.00330.0271.3211-0.15341.6768-0.06570.2101-0.5138-0.2783-0.0637-0.22390.88580.35550.1260.78020.13510.0040.3398-0.07330.56599.1314100.8109-12.2537
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and peptide)A0
2X-RAY DIFFRACTION2(chain 'B' and peptide)B0
3X-RAY DIFFRACTION3(chain 'C' and peptide)C0
4X-RAY DIFFRACTION4(chain 'D' and peptide)D0
5X-RAY DIFFRACTION5(chain 'E' and peptide)E0

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