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- PDB-6vct: Mucor circinelloides FKBP12 protein bound with APX879 in C2221 sp... -

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Basic information

Entry
Database: PDB / ID: 6vct
TitleMucor circinelloides FKBP12 protein bound with APX879 in C2221 space group
ComponentsPeptidylprolyl isomerase
KeywordsISOMERASE / FK506-binding protein 1A / FKBP12 / FK506
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cytoplasm
Similarity search - Function
: / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Chem-R27 / peptidylprolyl isomerase
Similarity search - Component
Biological speciesMucor circinelloides (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsGobeil, S. / Spicer, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1-AI112595-04 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)PO1-AI104533-04 United States
Citation
Journal: Mbio / Year: 2021
Title: Leveraging Fungal and Human Calcineurin-Inhibitor Structures, Biophysical Data, and Dynamics To Design Selective and Nonimmunosuppressive FK506 Analogs.
Authors: Gobeil, S.M. / Bobay, B.G. / Juvvadi, P.R. / Cole, D.C. / Heitman, J. / Steinbach, W.J. / Venters, R.A. / Spicer, L.D.
#1: Journal: Biorxiv / Year: 2020
Title: Designing Selective and Non-Immunosuppressive Antifungal FK506 Analogs: Structures, Biophysics and Dynamics of Fungal and Human Calcineurin-Inhibitor Complexes
Authors: Gobeil, S.M. / Bobay, B.G. / Juvvadi, P.R. / Cole, D.C. / Heitman, J. / Steinbach, W.J. / Venters, R.A. / Spicer, L.D.
History
DepositionDec 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: 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: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9562
Polymers12,0961
Non-polymers8601
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, A stoichiometry of 1 was obtained for this ligand, gel filtration, The protein elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.533, 75.544, 46.543
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-315-

HOH

21A-369-

HOH

31A-380-

HOH

41A-384-

HOH

51A-398-

HOH

61A-403-

HOH

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Components

#1: Protein Peptidylprolyl isomerase


Mass: 12095.665 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mucor circinelloides (fungus) / Gene: fkbA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U3N5X4, peptidylprolyl isomerase
#2: Chemical ChemComp-R27 / N'-[(3S,4R,5S,8R,9E,12S,14S,15R,16S,18R,19R,26aS)-5,19-dihydroxy-3-{(1E)-1-[(1R,3R,4R)-4-hydroxy-3-methoxycyclohexyl]prop-1-en-2-yl}-14,16-dimethoxy-4,10,12,18-tetramethyl-1,20,21-trioxo-8-(prop-2-en-1-yl)-1,3,4,5,6,8,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,26a-docosahydro-7H-15,19-epoxypyrido[2,1-c][1,4]oxazacyclotricosin-7-ylidene]acetohydrazide / APX879


Mass: 860.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H73N3O12 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1600mM Sodium Citrate Tribasic

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 7938 / % possible obs: 100 % / Redundancy: 14.5 % / Biso Wilson estimate: 17.55 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.021 / Rrim(I) all: 0.08 / Rsym value: 0.078 / Net I/av σ(I): 56.9 / Net I/σ(I): 56.9
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 19.1 / Num. unique obs: 385 / CC1/2: 0.994 / Rpim(I) all: 0.045 / Rrim(I) all: 0.176 / Rsym value: 0.17 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HUA

5hua


Resolution: 1.94→32.81 Å / SU ML: 0.1546 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.0015
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206 792 10 %
Rwork0.1537 7131 -
obs0.1587 7923 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.97 Å2
Refinement stepCycle: LAST / Resolution: 1.94→32.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 61 120 1003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059903
X-RAY DIFFRACTIONf_angle_d1.06781225
X-RAY DIFFRACTIONf_chiral_restr0.0567136
X-RAY DIFFRACTIONf_plane_restr0.0048157
X-RAY DIFFRACTIONf_dihedral_angle_d25.6571151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.060.2051270.1461144X-RAY DIFFRACTION98.6
2.06-2.220.18751320.1431183X-RAY DIFFRACTION100
2.22-2.440.22711290.14071163X-RAY DIFFRACTION99.92
2.44-2.80.22331330.15711192X-RAY DIFFRACTION99.92
2.8-3.520.21141310.15621189X-RAY DIFFRACTION100
3.52-32.810.19491400.16071260X-RAY DIFFRACTION99.86

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