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- PDB-7ogi: Human Cyclophilin D in complex with N-(5-ethyl-4-oxo-1,2,3,4,5,6-... -

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Basic information

Entry
Database: PDB / ID: 7ogi
TitleHuman Cyclophilin D in complex with N-(5-ethyl-4-oxo-1,2,3,4,5,6-hexahydro-1,5-benzodiazocin-8-yl)-7methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide
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 / : / 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 proton-transporting ATPase activity, rotational mechanism / : / 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 / apoptotic mitochondrial changes / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / necroptotic process / negative regulation of intrinsic apoptotic signaling pathway / cellular response to calcium ion / peptide binding / peptidyl-prolyl cis-trans isomerase activity / response to ischemia / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / 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
Chem-VDH / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsSilva, D.O. / Graedler, U. / Bandeiras, T.M.
CitationJournal: To Be Published
Title: Human Cyclophilin D in complex with N-(5-ethyl-4-oxo-1,2,3,4,5,6-hexahydro-1,5-benzodiazocin-8-yl)-7methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide
Authors: Silva, D.O. / Graedler, U. / Bandeiras, T.M.
History
DepositionMay 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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)18,4504
Polymers17,7831
Non-polymers6673
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint7 kcal/mol
Surface area7150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.735, 56.735, 87.305
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-582-

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-VDH / N-(5-ethyl-4-oxidanylidene-1,2,3,6-tetrahydro-1,5-benzodiazocin-8-yl)-7-methyl-2-oxidanylidene-1H-pyrazolo[1,5-a]pyrimidine-6-carboxamide / N-(5-ethyl-4-oxo-1,2,3,4,5,6-hexahydro-1,5-benzodiazocin-8-yl)-7methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide


Mass: 394.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / 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
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.01 Å3/Da / Density % sol: 38.88 %
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: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96545 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96545 Å / Relative weight: 1
ReflectionResolution: 1.01→47.57 Å / Num. obs: 71086 / % possible obs: 94.44 % / Redundancy: 6.2 % / Biso Wilson estimate: 7.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.81
Reflection shellResolution: 1.01→1.046 Å / Num. unique obs: 4404 / CC1/2: 0.663

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NHB

7nhb
PDB Unreleased entry


Resolution: 1.01→47.57 Å / SU ML: 0.0777 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.8564
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1435 1165 1.64 %
Rwork0.1352 69917 -
obs0.1353 71082 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.48 Å2
Refinement stepCycle: LAST / Resolution: 1.01→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 46 282 1568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621314
X-RAY DIFFRACTIONf_angle_d1.0161768
X-RAY DIFFRACTIONf_chiral_restr0.0833187
X-RAY DIFFRACTIONf_plane_restr0.0073229
X-RAY DIFFRACTIONf_dihedral_angle_d11.2179495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.060.2702970.23465774X-RAY DIFFRACTION63.27
1.06-1.110.18571410.16678505X-RAY DIFFRACTION93.33
1.11-1.180.15591510.12439020X-RAY DIFFRACTION98.45
1.18-1.270.1361520.11949143X-RAY DIFFRACTION99.94
1.27-1.40.15491530.12529195X-RAY DIFFRACTION99.96
1.4-1.60.13061550.12119261X-RAY DIFFRACTION99.93
1.6-2.020.14181550.13279336X-RAY DIFFRACTION99.95
2.02-47.570.12951610.13599683X-RAY DIFFRACTION99.63

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