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- PDB-6vcv: Aspergillus fumigatus FKBP12 protein bound with APX879 in P1 spac... -

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Basic information

Entry
Database: PDB / ID: 6vcv
TitleAspergillus fumigatus FKBP12 protein bound with APX879 in P1 space group
ComponentsFK506-binding protein 1A
KeywordsISOMERASE / FK506-binding protein 1A / FKBP12 / APX879
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nucleus / cytosol / 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 / FK506-binding protein 1A
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: FK506-binding protein 1A
B: FK506-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5724
Polymers24,8522
Non-polymers1,7202
Water5,981332
1
A: FK506-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2862
Polymers12,4261
Non-polymers8601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FK506-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2862
Polymers12,4261
Non-polymers8601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.562, 39.620, 40.771
Angle α, β, γ (deg.)76.823, 89.918, 85.744
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein FK506-binding protein 1A / FKBP / Peptidyl-prolyl cis-trans isomerase / PPIase / Rapamycin-binding protein


Mass: 12425.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: fpr1A, AFUA_6G12170 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4WLV6, 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.: 2 / Source method: obtained synthetically / Formula: C46H73N3O12 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 5mM MES, 200mM zinc acetate, 15% reagent alcohol

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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: 1.6→50 Å / Num. obs: 27429 / % possible obs: 96.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 11.54 Å2 / CC1/2: 0.986 / Rpim(I) all: 0.073 / Rrim(I) all: 0.114 / Net I/σ(I): 33.9
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 17.2 / Num. unique obs: 1337 / CC1/2: 0.94 / Rpim(I) all: 0.115 / Rrim(I) all: 0.178

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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: 5HWB

5hwb


Resolution: 1.6→27.12 Å / SU ML: 0.1453 / Cross valid method: FREE R-VALUE / σ(F): 2.1 / Phase error: 21.1618
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2136 2019 7.36 %
Rwork0.1765 25404 -
obs0.1793 27423 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 122 332 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671860
X-RAY DIFFRACTIONf_angle_d1.34782526
X-RAY DIFFRACTIONf_chiral_restr0.0644282
X-RAY DIFFRACTIONf_plane_restr0.0066324
X-RAY DIFFRACTIONf_dihedral_angle_d22.2777672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.21711350.16631804X-RAY DIFFRACTION93.63
1.64-1.680.22151440.16331779X-RAY DIFFRACTION95.48
1.68-1.730.23181390.16071784X-RAY DIFFRACTION95.39
1.73-1.790.19871520.181841X-RAY DIFFRACTION96.05
1.79-1.850.21351430.17341817X-RAY DIFFRACTION96.27
1.85-1.930.21081510.17781772X-RAY DIFFRACTION95.81
1.93-2.020.19861320.17171814X-RAY DIFFRACTION96.43
2.02-2.120.24971390.17251817X-RAY DIFFRACTION95.69
2.12-2.260.19841540.17791829X-RAY DIFFRACTION96.87
2.26-2.430.20871430.18231821X-RAY DIFFRACTION97.08
2.43-2.670.24731440.19831837X-RAY DIFFRACTION97.92
2.67-3.060.21871530.19491859X-RAY DIFFRACTION98
3.06-3.850.21181360.16831847X-RAY DIFFRACTION97.4
3.85-27.120.19731540.16851783X-RAY DIFFRACTION95.32

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