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- PDB-6xp3: Structure of human PYCR1 complexed with cyclopentanecarboxylic acid -

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Basic information

Entry
Database: PDB / ID: 6xp3
TitleStructure of human PYCR1 complexed with cyclopentanecarboxylic 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 / proline biosynthetic process / 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
cyclopentanecarboxylic acid / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.93 Å
AuthorsTanner, J.J. / Bogner, A.N.
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)170,82811
Polymers170,2165
Non-polymers6136
Water7,945441
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)341,65722
Polymers340,43210
Non-polymers1,22512
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area58850 Å2
ΔGint-635 kcal/mol
Surface area87390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.702, 178.533, 87.657
Angle α, β, γ (deg.)90.000, 106.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

21A-556-

HOH

31E-515-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IQ0 / cyclopentanecarboxylic acid


Mass: 114.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 200 mM Li2SO4, 18% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 10 mM cyclopentanecarboxylic acid. Crystal was soaked in cryobuffer containing 20% ...Details: Reservoir contained 200 mM Li2SO4, 18% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 10 mM cyclopentanecarboxylic acid. Crystal was soaked in cryobuffer containing 20% PEG 200, and 100 mM cyclopentanecarboxylic acid.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.93→47.18 Å / Num. obs: 116598 / % possible obs: 96.7 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Net I/σ(I): 11.9 / Num. measured all: 408772 / Scaling rejects: 448
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
1.93-1.963.50.5612016057890.770.350.6641.897.6
10.57-47.183.60.01726317350.9990.010.0236.396.8

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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: 2IZZ

2izz


Resolution: 1.93→47.175 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 5709 4.94 %
Rwork0.1891 109862 -
obs0.1906 115571 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.82 Å2 / Biso mean: 34.9694 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: final / Resolution: 1.93→47.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9842 0 36 441 10319
Biso mean--37.11 32.39 -
Num. residues----1382
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.93-1.95190.34851620.3178372397
1.9519-1.97490.3141980.2677377299
1.9749-1.9990.25922050.2281377899
1.999-2.02430.26142030.22343798100
2.0243-2.05090.3811750.3493365495
2.0509-2.0790.45461370.3939298378
2.079-2.10870.2632080.2279377099
2.1087-2.14020.23972100.18843832100
2.1402-2.17360.25111930.1959377399
2.1736-2.20930.22351770.2054381399
2.2093-2.24740.54271550.4526281474
2.2474-2.28820.33281720.2781338087
2.2882-2.33220.21581950.18633782100
2.3322-2.37980.18741910.1683839100
2.3798-2.43160.21172290.17233764100
2.4316-2.48820.20871870.1765377999
2.4882-2.55040.24321890.1744363395
2.5504-2.61930.19521970.16763818100
2.6193-2.69640.20971690.1912344591
2.6964-2.78340.20022250.17073780100
2.7834-2.88290.19091990.1737380399
2.8829-2.99830.25072160.18123808100
2.9983-3.13470.20942080.17023813100
3.1347-3.30.19181680.1796365795
3.3-3.50660.20281990.1772347791
3.5066-3.77730.18311900.1678343191
3.7773-4.15720.18411900.1529340889
4.1572-4.75830.15911800.13573853100
4.7583-5.9930.19151900.17193843100
5.993-47.1750.15661920.1529383998
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)
10.57260.13960.74530.16220.04122.50080.0447-0.11780.02160.0742-0.0406-0.04690.10050.15950.00420.1103-0.0019-0.02420.1932-0.01140.186725.9873173.587124.0881
21.13080.2463-0.87030.4443-0.10731.80790.0769-0.0320.0643-0.1074-0.0064-0.1323-0.25650.3719-0.05510.1556-0.0309-0.01070.2323-0.01790.203532.8233183.2942-5.9765
30.4418-0.2542-0.03291.1177-0.10271.7513-0.1341-0.1612-0.14160.2701-0.0040.03830.5440.00010.10690.36210.04950.04470.17310.02270.219610.2547139.694218.754
40.9327-0.5088-0.40351.0570.42052.004-0.02660.0469-0.1019-0.1870.0062-0.17820.29570.59620.00350.25890.10080.02360.27220.01490.226426.2158145.3316-7.7892
50.81770.2241-0.61481.34680.03751.49610.1805-0.29250.17210.3518-0.1040.0526-0.40650.1994-0.03920.2559-0.0562-0.00010.2054-0.03450.20820.0503200.695915.8143
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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