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- PDB-8uc4: Apo X-ray crystal structure of Cyclophilin D with a surface entro... -

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Basic information

Entry
Database: PDB / ID: 8uc4
TitleApo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / Cyclophilin D / mitochondria
Function / homology
Function and homology information


: / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / mitochondrial depolarization / negative regulation of oxidative phosphorylation ...: / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / mitochondrial depolarization / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / apoptotic mitochondrial changes / necroptotic process / cellular response to calcium ion / response to ischemia / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cellular response to hydrogen peroxide / protein folding / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsKreitler, D.F. / Rangwala, A.M. / Seeliger, M.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119437 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F30CA260771 United States
CitationJournal: To Be Published
Title: Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)
Authors: Kreitler, D.F. / Seeliger, M.A. / Rangwala, A.M.
History
DepositionSep 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1626
Polymers17,8671
Non-polymers3,2955
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.959, 56.959, 109.781
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11X-205-

NA

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase F, mitochondrial / PPIase F / Cyclophilin D / CyP-D / CypD / Cyclophilin F / Mitochondrial cyclophilin / CyP-M / Rotamase F


Mass: 17867.334 Da / Num. of mol.: 1 / Mutation: K175I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30405, peptidylprolyl isomerase
#2: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.64 % / Description: 3D
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Well solution: 40% w/v PEG3350, 30 mM NaCl, 50 mM potassium phosphate monobasic pH 7.0 Protein Solution: 15 mg/mL protein, 20 mM Tris pH 8.0, 50 mM NaCl, 1 mM DTT, and 5% glycerol Drop: 1 uL ...Details: Well solution: 40% w/v PEG3350, 30 mM NaCl, 50 mM potassium phosphate monobasic pH 7.0 Protein Solution: 15 mg/mL protein, 20 mM Tris pH 8.0, 50 mM NaCl, 1 mM DTT, and 5% glycerol Drop: 1 uL protein solution, 1 uL well solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 18, 2022 / Details: KB
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.87→28.48 Å / Num. obs: 15443 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 23.25 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.137 / Net I/σ(I): 9.8
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 6.4 % / Num. unique obs: 1014 / CC1/2: 0.821 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX1.18rc7_3834refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→28.48 Å / SU ML: 0.1751 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2109 1539 10 %
Rwork0.1822 13855 -
obs0.185 15394 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.14 Å2
Refinement stepCycle: LAST / Resolution: 1.87→28.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 41 119 1401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061304
X-RAY DIFFRACTIONf_angle_d0.80021742
X-RAY DIFFRACTIONf_chiral_restr0.0564187
X-RAY DIFFRACTIONf_plane_restr0.0045223
X-RAY DIFFRACTIONf_dihedral_angle_d13.9257486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.930.24941270.20771146X-RAY DIFFRACTION92.05
1.93-20.24371360.19561225X-RAY DIFFRACTION100
2-2.080.23681380.17131233X-RAY DIFFRACTION99.93
2.08-2.180.22391380.17061251X-RAY DIFFRACTION100
2.18-2.290.21821410.16641259X-RAY DIFFRACTION100
2.29-2.440.19521380.161248X-RAY DIFFRACTION100
2.44-2.630.23241390.18311246X-RAY DIFFRACTION100
2.63-2.890.23291410.1741277X-RAY DIFFRACTION99.86
2.89-3.310.20251410.18431271X-RAY DIFFRACTION99.93
3.31-4.160.17691450.17921303X-RAY DIFFRACTION100
4.16-28.480.21711550.19691396X-RAY DIFFRACTION99.74

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