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- PDB-6xp2: Structure of human PYCR1 complexed with L-thiazolidine-4-carboxylate -

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Basic information

Entry
Database: PDB / ID: 6xp2
TitleStructure of human PYCR1 complexed with L-thiazolidine-4-carboxylate
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 / proline biosynthetic process / 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
THIOPROLINE / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 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)170,77010
Polymers170,2165
Non-polymers5555
Water3,729207
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)341,54120
Polymers340,43210
Non-polymers1,10910
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area58490 Å2
ΔGint-621 kcal/mol
Surface area90310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.157, 88.000, 115.789
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-514-

HOH

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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-PRS / THIOPROLINE


Type: L-peptide linking / Mass: 133.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Crystallization reservoir contained 250 mM Li2SO4, 19% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Crystal was soaked in cryobuffer containing 50 mM L-thiazolidine-4-carboxylate and 20% PEG 200.

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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: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.23 Å / Num. obs: 74689 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Net I/σ(I): 15.5 / Num. measured all: 515383 / Scaling rejects: 10
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
2.3-2.357.10.9153232345510.8480.3710.9892.2100
11.27-49.236.30.023462873110.010.02544.998.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5UAU

5uau


Resolution: 2.3→49.226 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 2268 3.06 %
Rwork0.198 71854 -
obs0.1995 74122 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.72 Å2 / Biso mean: 49.4633 Å2 / Biso min: 16.81 Å2
Refinement stepCycle: final / Resolution: 2.3→49.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9926 0 31 207 10164
Biso mean--51.59 36.51 -
Num. residues----1377
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.350.2861430.22264443100
2.35-2.40470.27031580.20874450100
2.4047-2.46480.25621320.2074488100
2.4648-2.53150.28151310.2284483100
2.5315-2.6060.23931210.20094491100
2.606-2.69010.31861210.2633442498
2.6901-2.78620.23311470.20674423100
2.7862-2.89770.2551520.20054501100
2.8977-3.02960.28921670.20944504100
3.0296-3.18930.24241480.20754465100
3.1893-3.38910.29441180.22364544100
3.3891-3.65070.28831420.2327437196
3.6507-4.01790.30931520.2221427095
4.0179-4.59890.18641450.15324571100
4.5989-5.79270.19631560.17024624100
5.7927-49.2260.2051350.16614802100
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)
10.8115-0.93390.56733.6788-0.50280.77040.00610.13760.2606-0.6675-0.0001-0.2126-0.10350.00480.00770.2951-0.02510.03830.34310.00840.3083-15.433659.0877-57.9856
21.04030.49720.39562.82480.45130.7090.02070.0994-0.2343-0.07180.0170.44470.1559-0.1115-0.04490.1986-0.0027-0.01480.3369-0.00670.3301-22.992728.2054-52.8661
31.0255-1.1994-0.22173.90520.32870.40220.00320.02140.037-0.22920.00980.5083-0.1716-0.1105-0.0210.2579-0.010.02820.3340.0010.325-32.31959.4505-24.0201
40.84631.1936-0.4663.1825-0.52350.83210.0336-0.0216-0.09640.4082-0.04160.18210.1967-0.09520.01410.29730.00730.06790.323-0.01340.3221-29.62628.1082-14.8117
50.60060.2143-0.12683.37771.02721.36350.0369-0.18220.26370.6022-0.01370.4567-0.1598-0.055-0.02380.43760.00320.06170.3445-0.01030.3272-4.678459.46733.1717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(peptide and chain A)A)0
2X-RAY DIFFRACTION2(peptide and chain B)B)0
3X-RAY DIFFRACTION3(peptide and chain C)C)0
4X-RAY DIFFRACTION4(peptide and chain D)D)0
5X-RAY DIFFRACTION5(peptide and chain E)E)0

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