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- PDB-6lhm: Structure of human PYCR2 -

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Basic information

Entry
Database: PDB / ID: 6lhm
TitleStructure of human PYCR2
ComponentsPyrroline-5-carboxylate reductase 2
KeywordsOXIDOREDUCTASE / PYCR2 / carboxylate / P5CR / decamer / pentamer / Pyrroline-5-carboxylate reductase
Function / homology
Function and homology information


pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / Glutamate and glutamine metabolism / : / cellular response to oxidative stress / mitochondrial matrix / mitochondrion
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
Pyrroline-5-carboxylate reductase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBaburajendran, N.
CitationJournal: Neuron / Year: 2020
Title: Loss of PYCR2 Causes Neurodegeneration by Increasing Cerebral Glycine Levels via SHMT2.
Authors: Escande-Beillard, N. / Loh, A. / Saleem, S.N. / Kanata, K. / Hashimoto, Y. / Altunoglu, U. / Metoska, A. / Grandjean, J. / Ng, F.M. / Pomp, O. / Baburajendran, N. / Wong, J. / Hill, J. / ...Authors: Escande-Beillard, N. / Loh, A. / Saleem, S.N. / Kanata, K. / Hashimoto, Y. / Altunoglu, U. / Metoska, A. / Grandjean, J. / Ng, F.M. / Pomp, O. / Baburajendran, N. / Wong, J. / Hill, J. / Beillard, E. / Cozzone, P. / Zaki, M. / Kayserili, H. / Hamada, H. / Shiratori, H. / Reversade, B.
History
DepositionDec 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: Pyrroline-5-carboxylate reductase 2
B: Pyrroline-5-carboxylate reductase 2
C: Pyrroline-5-carboxylate reductase 2
D: Pyrroline-5-carboxylate reductase 2
E: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)158,6895
Polymers158,6895
Non-polymers00
Water00
1
A: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)31,7381
Polymers31,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)31,7381
Polymers31,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)31,7381
Polymers31,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)31,7381
Polymers31,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)31,7381
Polymers31,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.903, 110.312, 155.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
Pyrroline-5-carboxylate reductase 2 / P5CR 2


Mass: 31737.818 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PYCR2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96C36, pyrroline-5-carboxylate reductase

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Carboxylic acids, 0.1M Buffer system 3 pH 8.5, 50% v/v Precipitant Mix 3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.4→46.904 Å / Num. obs: 24754 / % possible obs: 97.68 % / Redundancy: 8.2 % / CC1/2: 0.829 / Net I/σ(I): 8.75
Reflection shellResolution: 3.4→3.522 Å / Num. unique obs: 20319 / CC1/2: 0.659

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZZ

2izz


Resolution: 3.4→46.904 Å / SU ML: 0.67 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.86
RfactorNum. reflection% reflection
Rfree0.3601 1961 8.11 %
Rwork0.3291 --
obs0.3317 24194 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.4 Å2 / Biso mean: 76.6374 Å2 / Biso min: 33.54 Å2
Refinement stepCycle: final / Resolution: 3.4→46.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9211 0 0 0 9211
Num. residues----1317
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4001-3.48510.62481270.5361138187
3.4851-3.57930.48851380.4558152996
3.5793-3.68460.49181260.4648155397
3.6846-3.80340.43481590.3996157398
3.8034-3.93930.51831230.4595148593
3.9393-4.0970.42611340.3449155998
4.097-4.28330.2881400.30841614100
4.2833-4.50890.32211410.29351613100
4.5089-4.79120.33231490.2921605100
4.7912-5.16070.33261340.29561644100
5.1607-5.67920.35071470.31461620100
5.6792-6.49920.35981470.30541643100
6.4992-8.18120.24361400.26081669100
8.1812-46.90.27581560.2459174599
Refinement TLS params.Method: refined / Origin x: -7.2772 Å / Origin y: 26.959 Å / Origin z: -20.3521 Å
111213212223313233
T0.1677 Å2-0.0273 Å20.0896 Å2-0.4808 Å20.0624 Å2--0.2764 Å2
L0.7275 °20.0245 °2-0.0856 °2-1.1188 °2-0.2362 °2--1.6924 °2
S-0.0276 Å °0.3163 Å °0.01 Å °-0.0785 Å °0.0705 Å °0.0407 Å °0.5312 Å °-0.2289 Å °-0.0099 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 271
2X-RAY DIFFRACTION1allB3 - 271
3X-RAY DIFFRACTION1allC3 - 271
4X-RAY DIFFRACTION1allD1 - 273
5X-RAY DIFFRACTION1allE10 - 273

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