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- PDB-7r2h: 0.79A resolution structure of DMSO bound Cyclophilin D -

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Basic information

Entry
Database: PDB / ID: 7r2h
Title0.79A resolution structure of DMSO bound Cyclophilin D
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / Cyclophilin D PPIase
Function / homology
Function and homology information


regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / 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 / mitochondrial depolarization / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation ...regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / 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 / mitochondrial depolarization / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / necroptotic process / negative regulation of intrinsic apoptotic signaling pathway / protein peptidyl-prolyl isomerization / cellular response to calcium ion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to ischemia / cellular response to hydrogen peroxide / protein folding / mitochondrial inner membrane / 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
Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.79 Å
AuthorsSilva, D.O. / Graedler, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 0.79A resolution structure of DMSO bound Cyclophilin D
Authors: Silva, D.O. / Graedler, U.
History
DepositionFeb 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,8612
Polymers17,7831
Non-polymers781
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint3 kcal/mol
Surface area7220 Å2
Unit cell
Length a, b, c (Å)57.348, 57.348, 87.562
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

21A-634-

HOH

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Components

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


Mass: 17783.322 Da / Num. of mol.: 1 / Mutation: K133I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P30405, peptidylprolyl isomerase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 15 % PEG 3350, 0.1M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.8265 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2018
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8265 Å / Relative weight: 1
ReflectionResolution: 0.79→36.8 Å / Num. obs: 148904 / % possible obs: 93.47 % / Redundancy: 5.2 % / Biso Wilson estimate: 6.59 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.96
Reflection shellResolution: 0.79→0.8182 Å / Num. unique obs: 12036 / CC1/2: 0.623

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASERccp4i 7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R8W

6r8w


Resolution: 0.79→36.8 Å / SU ML: 0.0736 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 14.7377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1549 7538 5.05 %
Rwork0.1434 141646 -
obs0.144 148902 93.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.78 Å2
Refinement stepCycle: LAST / Resolution: 0.79→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 4 335 1579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541291
X-RAY DIFFRACTIONf_angle_d0.90591743
X-RAY DIFFRACTIONf_chiral_restr0.0863189
X-RAY DIFFRACTIONf_plane_restr0.0066228
X-RAY DIFFRACTIONf_dihedral_angle_d11.0547466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.79-0.80.27451800.30233107X-RAY DIFFRACTION62.19
0.8-0.810.27541990.2823773X-RAY DIFFRACTION75.47
0.81-0.820.2532320.26524441X-RAY DIFFRACTION88.82
0.82-0.830.27632380.2554460X-RAY DIFFRACTION89.74
0.83-0.840.25792340.24994563X-RAY DIFFRACTION91.01
0.84-0.850.23062610.23084561X-RAY DIFFRACTION91.57
0.85-0.860.23242120.21024618X-RAY DIFFRACTION92.26
0.86-0.880.19052430.20014650X-RAY DIFFRACTION92.65
0.88-0.890.22682490.18894672X-RAY DIFFRACTION93.36
0.89-0.90.19882530.17394726X-RAY DIFFRACTION93.34
0.9-0.920.18822640.17084677X-RAY DIFFRACTION94.11
0.92-0.940.16392160.16484746X-RAY DIFFRACTION94.21
0.94-0.950.16232550.16014730X-RAY DIFFRACTION94.22
0.95-0.970.17562660.15634740X-RAY DIFFRACTION94.76
0.97-0.990.16452600.1524780X-RAY DIFFRACTION95.04
0.99-1.020.15832600.15044765X-RAY DIFFRACTION95.24
1.02-1.040.15292470.1444855X-RAY DIFFRACTION95.51
1.04-1.070.13552390.13814790X-RAY DIFFRACTION95.48
1.07-1.10.13532660.12784861X-RAY DIFFRACTION96.28
1.1-1.140.11572670.12074835X-RAY DIFFRACTION96.56
1.14-1.180.13142510.11834919X-RAY DIFFRACTION96.98
1.18-1.230.14952620.11974912X-RAY DIFFRACTION97.15
1.23-1.280.12572550.12154939X-RAY DIFFRACTION97.48
1.28-1.350.13262820.12634967X-RAY DIFFRACTION97.8
1.35-1.430.13012790.12644971X-RAY DIFFRACTION97.82
1.43-1.540.13942830.12694995X-RAY DIFFRACTION98.4
1.54-1.70.14942920.13734993X-RAY DIFFRACTION97.89
1.7-1.950.16192680.14625108X-RAY DIFFRACTION98.59
1.95-2.450.15282740.13985113X-RAY DIFFRACTION97.98
2.45-36.80.1592510.14045379X-RAY DIFFRACTION97.64

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