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- PDB-5uax: Structure of apo human PYCR-1 crystallized in space group C2 -

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Basic information

Entry
Database: PDB / ID: 5uax
TitleStructure of apo human PYCR-1 crystallized in space group C2
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
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 2.0May 1, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site.label_seq_id ..._atom_site.auth_seq_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity.pdbx_fragment / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 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

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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)170,39310
Polymers170,2165
Non-polymers1775
Water9,044502
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)340,78620
Polymers340,43210
Non-polymers35510
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area57600 Å2
ΔGint-623 kcal/mol
Surface area84850 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)68,1574
Polymers68,0862
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-120 kcal/mol
Surface area19960 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)68,1574
Polymers68,0862
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-121 kcal/mol
Surface area19740 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)68,1574
Polymers68,0862
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8880 Å2
ΔGint-121 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.850, 120.690, 88.140
Angle α, β, γ (deg.)90.000, 109.250, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-504-

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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 3 M NaCl and 0.1 M HEPES at pH 7.5-8.0 / PH range: 7.5-8.0

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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→60.345 Å / Num. obs: 153414 / % possible obs: 99.3 % / Redundancy: 4.4 % / Biso Wilson estimate: 24.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.85-1.882.90.6720.688195.9
10.13-60.346.30.0280.999196.8

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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→60.345 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.07
RfactorNum. reflection% reflection
Rfree0.1996 7615 4.96 %
Rwork0.1724 --
obs0.1738 153377 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.17 Å2 / Biso mean: 35.5291 Å2 / Biso min: 11.36 Å2
Refinement stepCycle: final / Resolution: 1.85→60.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9451 0 5 502 9958
Biso mean--30.77 36.26 -
Num. residues----1350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149650
X-RAY DIFFRACTIONf_angle_d1.27313159
X-RAY DIFFRACTIONf_chiral_restr0.081637
X-RAY DIFFRACTIONf_plane_restr0.0081705
X-RAY DIFFRACTIONf_dihedral_angle_d13.1045772
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8710.27942470.26894651489895
1.871-1.8930.29372650.25734777504298
1.893-1.91610.31342440.250549255169100
1.9161-1.94040.25772470.220548215068100
1.9404-1.96590.25952510.210448615112100
1.9659-1.99290.25352470.20148985145100
1.9929-2.02130.21062670.191848305097100
2.0213-2.05150.24212620.194948685130100
2.0515-2.08360.23222500.187748525102100
2.0836-2.11770.24482650.182649095174100
2.1177-2.15420.212670.186248745141100
2.1542-2.19340.22022610.179148615122100
2.1934-2.23560.21532390.171648865125100
2.2356-2.28120.21072460.168648385084100
2.2812-2.33080.19952370.16549265163100
2.3308-2.38510.20472300.169848615091100
2.3851-2.44470.20992630.17749265189100
2.4447-2.51080.18242700.160748565126100
2.5108-2.58470.20142530.159748415094100
2.5847-2.66810.23122460.175449115157100
2.6681-2.76350.22892510.18084844509599
2.7635-2.87410.19522420.17444890513299
2.8741-3.00490.22252540.181148825136100
3.0049-3.16330.2162630.17548935156100
3.1633-3.36150.19992650.172848655130100
3.3615-3.6210.18682520.164886513899
3.621-3.98540.15962600.14824836509699
3.9854-4.56190.15512720.14184788506098
4.5619-5.74680.17582480.16254838508697
5.7468-60.37710.17122510.1734868511997
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)
10.94980.5539-0.78281.0927-0.62661.72970.05410.150.1354-0.15680.0347-0.0794-0.2810.1539-0.08090.2058-0.04140.02130.193-0.01190.224720.0509163.1227-8.4301
20.40820.0663-0.15470.63470.19651.86720.0959-0.20010.10290.21320.0015-0.062-0.15750.2779-0.06950.1845-0.0563-0.00740.213-0.05430.229416.3545156.345922.3274
31.3682-0.1432-0.64570.46930.12671.354-0.00820.0201-0.0166-0.13680.0045-0.17050.06140.4508-0.00810.20640.08580.00780.30770.01280.229835.9074127.3056-2.6929
40.5686-0.03390.08140.3636-0.52151.7898-0.0251-0.2555-0.12820.0767-0.0087-0.02960.20250.15060.02610.21980.0955-0.0050.26420.03950.2322.614119.112724.3842
50.55050.05850.2261.1158-0.20761.1973-0.1070.1917-0.2635-0.3196-0.0587-0.18840.71150.28880.10490.56040.08580.10810.2205-0.02260.32597.669101.3304-12.2872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-7 - 270
2X-RAY DIFFRACTION2chain BB-2 - 270
3X-RAY DIFFRACTION3chain CC-5 - 270
4X-RAY DIFFRACTION4chain DD0 - 269
5X-RAY DIFFRACTION5chain EE1 - 270

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