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- PDB-7zdn: Human Cyclophilin D in complex with fragment -

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Basic information

Entry
Database: PDB / ID: 7zdn
TitleHuman Cyclophilin D in complex with fragment
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
Chem-IU0 / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSilva, D.O. / Graedler, U. / Bandeiras, T.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human Cyclophilin D in complex with fragment
Authors: Silva, D.O. / Graedler, U.
History
DepositionMar 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,9474
Polymers35,5652
Non-polymers3822
Water7,999444
1
A: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9732
Polymers17,7821
Non-polymers1911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9732
Polymers17,7821
Non-polymers1911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.412, 81.877, 113.395
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

21A-525-

HOH

31B-430-

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 / ...PPIase F / Cyclophilin D / CypD / Cyclophilin F / Mitochondrial cyclophilin / CyP-M / Rotamase F / Human Cyclophilin D


Mass: 17782.271 Da / Num. of mol.: 2 / Fragment: UNP residues 44-207 / Mutation: K125Q, 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-IU0 / (1~{R},9~{R},10~{S})-12-oxa-8-azatricyclo[7.3.1.0^{2,7}]trideca-2(7),3,5-trien-10-ol


Mass: 191.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 18 - 23 % PEG3350, 0.1 M TRIS-HCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.549→38.31 Å / Num. obs: 54498 / % possible obs: 98.29 % / Redundancy: 4.4 % / Biso Wilson estimate: 24.04 Å2 / CC1/2: 0.989 / Net I/σ(I): 8.14
Reflection shellResolution: 1.549→1.605 Å / Num. unique obs: 5020 / CC1/2: 0.604

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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: 7R2H

7r2h


Resolution: 1.55→38.31 Å / SU ML: 0.2392 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.226 2679 4.93 %
Rwork0.1899 51645 -
obs0.1918 54324 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.06 Å2
Refinement stepCycle: LAST / Resolution: 1.55→38.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 28 444 2952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842578
X-RAY DIFFRACTIONf_angle_d0.92913481
X-RAY DIFFRACTIONf_chiral_restr0.0591379
X-RAY DIFFRACTIONf_plane_restr0.0074453
X-RAY DIFFRACTIONf_dihedral_angle_d12.8477951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.36091120.33692165X-RAY DIFFRACTION78.68
1.58-1.610.33921460.3032733X-RAY DIFFRACTION99.38
1.61-1.640.36541330.2982721X-RAY DIFFRACTION99.44
1.64-1.670.36351390.31962723X-RAY DIFFRACTION99.58
1.67-1.710.30311640.27772718X-RAY DIFFRACTION99.69
1.71-1.760.28361580.26532718X-RAY DIFFRACTION99.58
1.76-1.80.27531540.24292760X-RAY DIFFRACTION99.86
1.8-1.860.27841310.22182762X-RAY DIFFRACTION99.66
1.86-1.920.23841280.21892735X-RAY DIFFRACTION99.48
1.92-1.990.26761380.21672754X-RAY DIFFRACTION99.55
1.99-2.060.2664990.22282768X-RAY DIFFRACTION99
2.06-2.160.20861430.19362731X-RAY DIFFRACTION99
2.16-2.270.20081280.18072729X-RAY DIFFRACTION98.04
2.27-2.420.22141510.17882705X-RAY DIFFRACTION97.14
2.42-2.60.22961490.17462658X-RAY DIFFRACTION96.73
2.6-2.860.23121390.17092794X-RAY DIFFRACTION99.76
2.86-3.280.23811630.16882763X-RAY DIFFRACTION99.66
3.28-4.130.18751470.16082836X-RAY DIFFRACTION99.43
4.13-38.310.1981570.17942872X-RAY DIFFRACTION98.22

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