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- PDB-6xp0: Structure of human PYCR1 complexed with N-formyl L-proline -

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Basic information

Entry
Database: PDB / ID: 6xp0
TitleStructure of human PYCR1 complexed with N-formyl L-proline
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
1-formyl-L-proline / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)170,93110
Polymers170,2165
Non-polymers7165
Water6,503361
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)341,86320
Polymers340,43210
Non-polymers1,43110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)164.630, 88.513, 115.462
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-521-

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-FPK / 1-formyl-L-proline


Type: L-peptide linking / Mass: 143.141 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
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 100 mM N-formyl L-proline and 20% PEG 200.
PH range: 7.5-8.0

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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 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→82.32 Å / Num. obs: 120287 / % possible obs: 97.8 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.048 / Rrim(I) all: 0.094 / Net I/σ(I): 7.2 / Num. measured all: 435036 / Scaling rejects: 5
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
1.95-1.983.81.3042272360450.4830.7741.5250.899.7
10.68-82.323.50.03928078020.9960.0230.04621.393.9

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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: 1.95→67.026 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 2289 1.9 %
Rwork0.1869 117913 -
obs0.1873 120202 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.86 Å2 / Biso mean: 52.039 Å2 / Biso min: 23.07 Å2
Refinement stepCycle: final / Resolution: 1.95→67.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9874 0 50 361 10285
Biso mean--51.47 45.02 -
Num. residues----1375
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-1.99240.37521560.3127467100
1.9924-2.03880.34011360.28247396100
2.0388-2.08970.26421690.2664743399
2.0897-2.14620.29491390.2496742499
2.1462-2.20940.26961560.2239744899
2.2094-2.28070.23471520.2048740999
2.2807-2.36220.2221440.194741399
2.3622-2.45680.21391410.1903743099
2.4568-2.56860.25181310.1936737198
2.5686-2.70410.29781150.1923736597
2.7041-2.87350.22381400.1989736197
2.8735-3.09540.22971650.2049730797
3.0954-3.40680.21811450.1896725296
3.4068-3.89980.1771380.1695720495
3.8998-4.91310.15231230.1467720293
4.9131-67.0260.17811390.1766743193
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)
10.6539-0.57490.34213.5929-0.38170.70.03480.14380.2383-0.6396-0.0371-0.0892-0.1140.01540.00710.3772-0.00270.01240.40050.02310.3558-15.764259.5168-58.324
20.83340.30770.19872.47480.27890.60950.00240.0303-0.2048-0.1768-0.00250.4320.1509-0.09630.0030.28240.0015-0.04820.35390.00430.348-23.010628.3875-52.9092
30.8196-0.7005-0.16252.91180.2650.44920.01090.02530.0657-0.12870.00720.4243-0.1898-0.0906-0.02070.32520.00270.02660.37250.00760.371-32.552559.7568-23.9005
40.63110.6336-0.18422.4474-0.37110.72990.0291-0.0677-0.1220.2881-0.0190.19120.1587-0.1007-0.01830.2751-0.00290.05150.3292-0.00360.3309-29.804328.5159-14.968
50.45270.17920.01483.29490.33590.52950.0072-0.17510.250.6853-0.02760.3985-0.1009-0.02050.0190.4779-0.00490.0580.3956-0.03530.3477-4.477259.48813.0186
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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