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- PDB-5uaw: Structure of apo human PYCR-1 crystallized in space group P21212 -

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Basic information

Entry
Database: PDB / ID: 5uaw
TitleStructure of apo human PYCR-1 crystallized in space group P21212
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
ProC C-terminal domain-like / ProC C-terminal domain-like fold / 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 Rossmann-like Domain ...ProC C-terminal domain-like / ProC C-terminal domain-like fold / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065546 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1.
Authors: Christensen, E.M. / Patel, S.M. / Korasick, D.A. / Campbell, A.C. / Krause, K.L. / Becker, D.F. / Tanner, J.J.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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)170,69610
Polymers170,2165
Non-polymers4805
Water10,233568
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)341,39220
Polymers340,43210
Non-polymers96110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area59130 Å2
ΔGint-673 kcal/mol
Surface area91190 Å2
MethodPISA
2
A: Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2784
Polymers68,0862
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-134 kcal/mol
Surface area20540 Å2
MethodPISA
3
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2784
Polymers68,0862
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-132 kcal/mol
Surface area20930 Å2
MethodPISA
4
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules

E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2784
Polymers68,0862
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9130 Å2
ΔGint-129 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.030, 88.140, 117.320
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-517-

HOH

DetailsThe authors state that based on analytical ultracentrifugation sedimentation velocity experiments, the protein is primarily a decamer at 6 mg/mL (180 micro molar based on monomer molecular weight). Lower molecular weight species are also observed at a protein concentration of 0.8 mg/mL.

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Components

#1: Protein
Pyrroline-5-carboxylate reductase 1, mitochondrial / / P5CR 1


Mass: 34043.156 Da / Num. of mol.: 5 / Fragment: residues 1-300
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 300 mM Na2SO4, 16-18% (w/v) polyethylene glycol (PEG) 3350, and 0.1 M HEPES at pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→64.685 Å / Num. obs: 144477 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 22.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.85-1.886.50.9020.789199.9
10.13-64.6811.80.0251199.6

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZZ

2izz


Resolution: 1.85→64.685 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.12
RfactorNum. reflection% reflection
Rfree0.2157 7099 4.92 %
Rwork0.1805 --
obs0.1822 144355 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.59 Å2 / Biso mean: 38.5305 Å2 / Biso min: 10.37 Å2
Refinement stepCycle: final / Resolution: 1.85→64.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9944 0 25 568 10537
Biso mean--26.84 34.49 -
Num. residues----1372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210156
X-RAY DIFFRACTIONf_angle_d1.15713792
X-RAY DIFFRACTIONf_chiral_restr0.0681667
X-RAY DIFFRACTIONf_plane_restr0.0071786
X-RAY DIFFRACTIONf_dihedral_angle_d15.0766124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.8710.29472470.266545394786
1.871-1.8930.33182320.258145384770
1.893-1.91610.31882370.255145114748
1.9161-1.94040.30282250.245545214746
1.9404-1.96590.3042360.236745294765
1.9659-1.99280.29192270.23345364763
1.9928-2.02130.2822360.225745034739
2.0213-2.05150.25242460.210545524798
2.0515-2.08360.2192220.197745254747
2.0836-2.11770.23352420.199845084750
2.1177-2.15420.21862270.195645654792
2.1542-2.19340.22982540.189445314785
2.1934-2.23560.22042540.182345284782
2.2356-2.28120.20272220.184945774799
2.2812-2.33080.23422320.18445424774
2.3308-2.38510.22342350.182845554790
2.3851-2.44470.24412380.181345524790
2.4447-2.51080.22992290.176345584787
2.5108-2.58470.22482440.176545434787
2.5847-2.66810.21492420.174545904832
2.6681-2.76350.19472270.176345614788
2.7635-2.87410.21122460.177745734819
2.8741-3.00490.23222300.180145914821
3.0049-3.16340.19412340.176845784812
3.1634-3.36150.22412270.188246274854
3.3615-3.62110.2072310.169846084839
3.6211-3.98540.20962560.157646364892
3.9854-4.5620.1662390.142446644903
4.562-5.74710.18892340.159347064940
5.7471-64.72420.17892480.175149095157
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)
10.8073-0.5690.27372.4901-0.10440.61040.02520.13830.2661-0.5656-0.01650.0004-0.14140.02280.0020.23950.0022-0.01110.20980.02280.2221-15.758559.2036-57.8782
21.2230.62470.33341.82420.46640.61610.04160.0454-0.2898-0.0776-0.03030.24820.14-0.0984-0.02070.15550.0184-0.04380.197-0.01280.2641-23.044228.1583-53.1617
30.7594-0.7744-0.15482.55640.35890.55060.020.0330.0887-0.0897-0.03410.4662-0.1877-0.1396-0.01130.18370.01090.04520.21-0.0030.2949-32.368359.4378-24.0538
40.68970.8096-0.32931.9623-0.43190.7555-0.0018-0.071-0.10280.2638-0.03430.19670.2156-0.09340.04380.2374-0.00230.09450.2011-0.01810.2557-29.544128.1214-14.8948
50.75720.2536-0.13051.80340.54660.94490.0771-0.19540.2790.4853-0.08350.3077-0.1909-0.0392-0.01370.4103-0.01680.07240.2355-0.03610.2232-4.677659.58963.2477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 274
2X-RAY DIFFRACTION2chain BB-5 - 275
3X-RAY DIFFRACTION3chain CC1 - 274
4X-RAY DIFFRACTION4chain DD-2 - 275
5X-RAY DIFFRACTION5chain EE0 - 275

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