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- PDB-6ybm: Scaffold-ligand complex with ligand unmodelled. -

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Basic information

Entry
Database: PDB / ID: 6ybm
TitleScaffold-ligand complex with ligand unmodelled.
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / N/A
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 / necroptotic process / apoptotic mitochondrial changes / 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-like / Cyclophilin / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsZacharchenko, T. / Lian, L.Y.
CitationJournal: To Be Published
Title: Scaffold-ligand complex with ligand unmodelled.
Authors: Zacharchenko, T. / Lian, L.Y.
History
DepositionMar 17, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionApr 15, 2020ID: 6GJX
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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
C: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7287
Polymers53,3503
Non-polymers3784
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint5 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.521, 58.635, 103.293
Angle α, β, γ (deg.)90.000, 124.852, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-444-

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.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Production host: Homo sapiens (human) / References: UniProt: P30405, peptidylprolyl isomerase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.41→62.7 Å / Num. obs: 118357 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 16.66 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 9.6
Reflection shellResolution: 1.41→1.45 Å / Num. unique obs: 8731 / CC1/2: 0.671 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CBT

5cbt


Resolution: 1.41→62.7 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.7342
RfactorNum. reflection% reflection
Rfree0.2112 5831 4.94 %
Rwork0.1779 --
obs0.1796 118024 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.4 Å2
Refinement stepCycle: LAST / Resolution: 1.41→62.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 25 527 4272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473887
X-RAY DIFFRACTIONf_angle_d0.725245
X-RAY DIFFRACTIONf_chiral_restr0.077569
X-RAY DIFFRACTIONf_plane_restr0.0046685
X-RAY DIFFRACTIONf_dihedral_angle_d12.53931424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.38662100.32883578X-RAY DIFFRACTION95.97
1.43-1.440.32542000.30433657X-RAY DIFFRACTION97.52
1.44-1.460.30521930.27043663X-RAY DIFFRACTION98.64
1.46-1.480.29382070.26533681X-RAY DIFFRACTION99.18
1.48-1.50.29771870.26183755X-RAY DIFFRACTION99.55
1.5-1.520.29242040.25343672X-RAY DIFFRACTION99.56
1.52-1.540.33082130.24283751X-RAY DIFFRACTION99.6
1.54-1.560.30651610.23483722X-RAY DIFFRACTION99.59
1.56-1.590.27351990.21883748X-RAY DIFFRACTION99.75
1.59-1.610.28161950.21173771X-RAY DIFFRACTION99.87
1.61-1.640.2471930.20223700X-RAY DIFFRACTION99.74
1.64-1.670.3081990.19913714X-RAY DIFFRACTION99.85
1.67-1.70.28971860.2013744X-RAY DIFFRACTION99.82
1.7-1.740.25982020.20413743X-RAY DIFFRACTION99.8
1.74-1.780.24011910.18853789X-RAY DIFFRACTION99.65
1.78-1.820.21271740.19073690X-RAY DIFFRACTION99.56
1.82-1.860.26351700.19293780X-RAY DIFFRACTION99.62
1.86-1.910.21931900.18133747X-RAY DIFFRACTION99.7
1.91-1.970.2142110.16663738X-RAY DIFFRACTION99.87
1.97-2.030.1942160.16373708X-RAY DIFFRACTION99.59
2.03-2.110.22092080.16133738X-RAY DIFFRACTION99.85
2.11-2.190.21051740.15813774X-RAY DIFFRACTION99.55
2.19-2.290.19812120.15493717X-RAY DIFFRACTION99.47
2.29-2.410.19881980.16223757X-RAY DIFFRACTION99.95
2.41-2.560.19432200.16453772X-RAY DIFFRACTION99.8
2.56-2.760.20061930.16853739X-RAY DIFFRACTION99.82
2.76-3.040.18941610.16993795X-RAY DIFFRACTION99.85
3.04-3.480.18081670.16083851X-RAY DIFFRACTION99.78
3.48-4.380.16371760.15573814X-RAY DIFFRACTION99.85
4.38-62.70.18482210.17683885X-RAY DIFFRACTION99.93

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