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- PDB-6xp1: Structure of human PYCR1 complexed with L-thiazolidine-2-carboxylate -

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Basic information

Entry
Database: PDB / ID: 6xp1
TitleStructure of human PYCR1 complexed with L-thiazolidine-2-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 / 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
(2S)-1,3-thiazolidine-2-carboxylic acid / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 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)170,73310
Polymers170,2165
Non-polymers5175
Water7,188399
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)341,46620
Polymers340,43210
Non-polymers1,03510
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area58660 Å2
ΔGint-654 kcal/mol
Surface area92430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.364, 88.298, 116.914
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-511-

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-T2C / (2S)-1,3-thiazolidine-2-carboxylic acid


Mass: 133.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
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 D,L-thiazolidine-2-carboxylate and 20% PEG 200.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→95.27 Å / Num. obs: 170953 / % possible obs: 99.8 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.023 / Rrim(I) all: 0.056 / Net I/σ(I): 13.4 / Num. measured all: 957039 / Scaling rejects: 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
1.75-1.785.61.8324688283980.4540.8472.0230.999.9
9.59-95.275.20.023598111430.9990.0110.02547.597.2

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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: 1.75→67.234 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 3521 2.06 %
Rwork0.1844 167290 -
obs0.1849 170811 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.18 Å2 / Biso mean: 53.2896 Å2 / Biso min: 22.81 Å2
Refinement stepCycle: final / Resolution: 1.75→67.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9947 0 28 399 10374
Biso mean--45.96 48.31 -
Num. residues----1378
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.7740.38141380.34956652100
1.774-1.79930.40131310.33566671100
1.7993-1.82620.36711470.32296620100
1.8262-1.85470.29161400.29946643100
1.8547-1.88510.3041520.27616650100
1.8851-1.91760.2941250.2556664100
1.9176-1.95250.26881210.24196621100
1.9525-1.99010.27371510.23326602100
1.9901-2.03070.25341500.22546679100
2.0307-2.07480.26741400.21526640100
2.0748-2.12310.23051630.20596658100
2.1231-2.17620.24481210.2076670100
2.1762-2.23510.21671520.19236662100
2.2351-2.30080.25531400.1896671100
2.3008-2.37510.20781380.18696703100
2.3751-2.460.20451370.19116705100
2.46-2.55850.22451440.17966685100
2.5585-2.67490.21681210.1876709100
2.6749-2.8160.16971610.19176690100
2.816-2.99240.25821250.26759100
2.9924-3.22340.20081220.19546744100
3.2234-3.54780.21261370.18826784100
3.5478-4.06110.19691570.1649673399
4.0611-5.11630.1721720.1401670398
5.1163-67.2340.18481360.1638697298
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)
10.5983-0.64160.41113.7045-0.38650.70070.0160.12970.2182-0.66940.0116-0.0964-0.13990.0035-0.01550.363-0.00690.03280.39110.01310.3629-15.722359.1787-58.3604
20.91250.51820.24342.03650.3010.53560.0150.0798-0.2184-0.06880.00820.30590.14-0.0975-0.02110.25570.0035-0.02340.3581-0.00630.3708-23.17928.3297-53.2114
30.654-0.8604-0.12942.80970.33250.40670.0004-0.00080.0555-0.0813-0.02140.3858-0.1541-0.11080.02010.3303-0.00310.05950.3686-0.0090.4137-32.530359.4915-24.3871
40.58680.7229-0.26441.8976-0.38340.68870.0132-0.0293-0.10340.3022-0.01740.18570.1723-0.10470.00310.3565-0.00610.0980.342-0.01770.3772-29.738728.3527-15.0196
50.50580.1456-0.10312.7540.76241.00170.0374-0.15410.24010.608-0.04530.3899-0.164-0.05270.00280.5859-0.00180.06730.3739-0.01680.3561-4.721659.73822.9252
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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