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- PDB-6vrx: Mucor circinelloides FKBP12 protein bound with FK506 in P3221 spa... -

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Basic information

Entry
Database: PDB / ID: 6vrx
TitleMucor circinelloides FKBP12 protein bound with FK506 in P3221 space group
ComponentsPeptidylprolyl isomeraseProlyl isomerase
KeywordsISOMERASE / FK506-binding protein 1A / FKBP12 / FK506
Function / homologyFKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / peptidylprolyl isomerase
Function and homology information
Biological speciesMucor circinelloides (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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
DepositionFeb 10, 2020Deposition 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
B: Peptidylprolyl isomerase
C: Peptidylprolyl isomerase
D: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5998
Polymers48,3834
Non-polymers3,2164
Water54030
1
A: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9002
Polymers12,0961
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9002
Polymers12,0961
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9002
Polymers12,0961
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9002
Polymers12,0961
Non-polymers8041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Peptidylprolyl isomerase
C: Peptidylprolyl isomerase
D: Peptidylprolyl isomerase
hetero molecules

B: Peptidylprolyl isomerase
C: Peptidylprolyl isomerase
D: Peptidylprolyl isomerase
hetero molecules

A: Peptidylprolyl isomerase
hetero molecules

A: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,19716
Polymers96,7658
Non-polymers6,4328
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
crystal symmetry operation2_544-y,x-y-1,z-1/31
crystal symmetry operation4_545y,x-1,-z1
Buried area21680 Å2
ΔGint-73 kcal/mol
Surface area32360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.905, 104.905, 111.613
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein
Peptidylprolyl isomerase / Prolyl isomerase


Mass: 12095.665 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Nterminal GSH are from the expression tag / Source: (gene. exp.) Mucor circinelloides (fungus) / Gene: fkbA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U3N5X4, peptidylprolyl isomerase
#2: Chemical
ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506 / Tacrolimus


Mass: 804.018 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H69NO12 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.75 Å3/Da / Density % sol: 67.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2100 mM DL Malic acid

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 23722 / % possible obs: 99.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 54.87 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.043 / Rrim(I) all: 0.13 / Rsym value: 0.123 / Net I/σ(I): 27.1
Reflection shellResolution: 2.54→2.59 Å / Redundancy: 1 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1167 / CC1/2: 0.806 / Rpim(I) all: 0.319 / Rsym value: 0.974 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HUA

5hua


Resolution: 2.54→37.2 Å / SU ML: 0.3336 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 24.329 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2442 1995 8.42 %
Rwork0.1968 21699 -
obs0.2008 23694 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.67 Å2
Refinement stepCycle: LAST / Resolution: 2.54→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 228 30 3520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743570
X-RAY DIFFRACTIONf_angle_d1.14984853
X-RAY DIFFRACTIONf_chiral_restr0.0554542
X-RAY DIFFRACTIONf_plane_restr0.005625
X-RAY DIFFRACTIONf_dihedral_angle_d14.65212145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.610.2671340.25431464X-RAY DIFFRACTION96.38
2.61-2.680.34011440.25591541X-RAY DIFFRACTION100
2.68-2.760.32191410.23451525X-RAY DIFFRACTION100
2.76-2.850.32031440.23711543X-RAY DIFFRACTION100
2.85-2.950.30031400.22271530X-RAY DIFFRACTION99.94
2.95-3.060.28931400.22971539X-RAY DIFFRACTION100
3.06-3.20.26621440.22231539X-RAY DIFFRACTION99.76
3.2-3.370.27851380.20121554X-RAY DIFFRACTION99.82
3.37-3.580.25191400.19611527X-RAY DIFFRACTION99.46
3.58-3.860.2711450.19741547X-RAY DIFFRACTION99.94
3.86-4.250.21471430.1771570X-RAY DIFFRACTION99.94
4.25-4.860.18641450.1561560X-RAY DIFFRACTION99.94
4.86-6.120.23171450.16981601X-RAY DIFFRACTION100
6.12-37.20.21921520.2161659X-RAY DIFFRACTION99.72

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