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- PDB-2wfj: Atomic resolution crystal structure of the PPIase domain of human... -

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Basic information

Entry
Database: PDB / ID: 2wfj
TitleAtomic resolution crystal structure of the PPIase domain of human cyclophilin G in complex with cyclosporin A.
Components
  • CYCLOSPORIN ACiclosporin
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE G
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN
Function / homology
Function and homology information


cyclosporin A binding / protein peptidyl-prolyl isomerization / mRNA Splicing - Major Pathway / RNA splicing / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nuclear matrix / SARS-CoV-1 activates/modulates innate immune responses / protein folding / nuclear speck ...cyclosporin A binding / protein peptidyl-prolyl isomerization / mRNA Splicing - Major Pathway / RNA splicing / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nuclear matrix / SARS-CoV-1 activates/modulates innate immune responses / protein folding / nuclear speck / RNA binding / nucleoplasm / nucleus / cytosol / 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
Cyclosporin A / : / Peptidyl-prolyl cis-trans isomerase G
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.75 Å
AuthorsStegmann, C.M. / Sheldrick, G.M. / Wahl, M.C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: The Thermodynamic Influence of Trapped Water Molecules on a Protein-Ligand Interaction.
Authors: Stegmann, C.M. / Seeliger, D. / Sheldrick, G.M. / De Groot, B.L. / Wahl, M.C.
History
DepositionApr 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Nov 30, 2012Group: Other
Revision 1.4May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE G
B: CYCLOSPORIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2106
Polymers21,0642
Non-polymers1464
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-7.4 kcal/mol
Surface area9890 Å2
MethodPQS
Unit cell
Length a, b, c (Å)37.319, 64.913, 69.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE G / CYCLOPHILIN G / CLK-ASSOCIATING RS-CYCLOPHILIN / CASP10 / PEPTIDYL-PROLYL ISOMERASE G / PPIASE G / ...CYCLOPHILIN G / CLK-ASSOCIATING RS-CYCLOPHILIN / CASP10 / PEPTIDYL-PROLYL ISOMERASE G / PPIASE G / ROTAMASE G / CARS-CYCLOPHILIN / CARS-CYP / SR-CYCLOPHILIN / SR-CYP / SRCYP


Mass: 19843.518 Da / Num. of mol.: 1 / Fragment: PPIASE DOMAIN, RESIDUES 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA (DE3) (NOVAGEN) / References: UniProt: Q13427, peptidylprolyl isomerase
#2: Protein/peptide CYCLOSPORIN A / Ciclosporin / CYCLOSPORINE / CICLOSPORIN / CICLOSPORINE / Ciclosporin


Type: Cyclic peptide / Class: ImmunosuppressantImmunosuppressive drug / Mass: 1220.625 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.
Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A

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Non-polymers , 4 types, 302 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) ...CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: CYCLOSPORIN A CHAIN: B COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 11 DESCRIPTION: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.
Sequence detailsINITIAL GA RESIDUES ARE CLONING ARTEFACTS.

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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: 1.87 Å3/Da / Density % sol: 34.4 %
Description: STRUCTURE WAS SOLVED BY APPLYING DIRECT METHODS IN SHELXD IN TWO STAGES FIRST SEARCHING FOR 9 SULFUR ATOMS WITH THE HELP OF PATTERSON SEEDING AND DUAL-SPACE DIRECT METHODS AND THEN ...Description: STRUCTURE WAS SOLVED BY APPLYING DIRECT METHODS IN SHELXD IN TWO STAGES FIRST SEARCHING FOR 9 SULFUR ATOMS WITH THE HELP OF PATTERSON SEEDING AND DUAL-SPACE DIRECT METHODS AND THEN EXPANDING THE MOST PROMISING SOLUTIONS TO THE FULL STRUCTURE. DATA WERE COLLECTED FROM A SINGLE CRYSTAL FIRST ON A BRUKER ROTATING-ANODE GENERATOR, PRODUCING CUKALPHA RADIATION, AND A SMART6000 16-MEGAPIXEL CCD TO A RESOLUTION OF 1.12A. DATA FROM THE SAME CRYSTAL WERE THEN COLLECTED ON BEAMLINE PXII OF THE SWISS LIGHT SOURCE (SLS, VILLIGEN, SWITZERLAND) USING A MAR CCD 225 DETECTOR AND MERGED WITH THE IN-HOUSE DATA.
Crystal growpH: 8.5
Details: 28-32% (W/V) PEG 4000, 0.2M MGCL2, 0.1M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.6888
DetectorType: MARRESEARCH / Detector: CCD / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 0.75→40 Å / Num. obs: 212972 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.25 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.6
Reflection shellResolution: 0.75→0.78 Å / Redundancy: 3.43 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.63 / % possible all: 90.4

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
SHELXphasing
RefinementMethod to determine structure: DIRECT METHODS
Starting model: NONE

Resolution: 0.75→10 Å / Num. parameters: 16518 / Num. restraintsaints: 21007 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.129 10644 5 %RANDOM
all0.112 212742 --
obs0.111 -99.1 %-
Refine analyzeNum. disordered residues: 20 / Occupancy sum hydrogen: 1253.37 / Occupancy sum non hydrogen: 1660.65
Refinement stepCycle: LAST / Resolution: 0.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 6 298 1732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.108
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.052
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.115

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