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- PDB-5i98: Structure of apo FKBP12(P104G) from C. albicans -

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Basic information

Entry
Database: PDB / ID: 5i98
TitleStructure of apo FKBP12(P104G) from C. albicans
ComponentsFK506-binding protein 1
KeywordsISOMERASE / FKBP12 / Self-catalysis
Function / homology
Function and homology information


negative regulation of homoserine biosynthetic process / : / fungal biofilm matrix / macrolide binding / nonfunctional rRNA decay / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific ...negative regulation of homoserine biosynthetic process / : / fungal biofilm matrix / macrolide binding / nonfunctional rRNA decay / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / extracellular region / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #40 / : / Chitinase A; domain 3 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
FK506-binding protein 1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.999 Å
AuthorsSchumacher, M.A.
CitationJournal: Mbio / Year: 2016
Title: Structures of Pathogenic Fungal FKBP12s Reveal Possible Self-Catalysis Function.
Authors: Tonthat, N.K. / Juvvadi, P.R. / Zhang, H. / Lee, S.C. / Venters, R. / Spicer, L. / Steinbach, W.J. / Heitman, J. / Schumacher, M.A.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: FK506-binding protein 1
B: FK506-binding protein 1


Theoretical massNumber of molelcules
Total (without water)25,6752
Polymers25,6752
Non-polymers00
Water2,900161
1
A: FK506-binding protein 1


Theoretical massNumber of molelcules
Total (without water)12,8381
Polymers12,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FK506-binding protein 1


Theoretical massNumber of molelcules
Total (without water)12,8381
Polymers12,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.225, 43.963, 56.989
Angle α, β, γ (deg.)90.000, 115.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 12837.553 Da / Num. of mol.: 2 / Mutation: P104G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876
Gene: RBP1, RBP11, CaO19.11186, CaO19.3702, RBP2, RBP12, CaJ7.0299, CaO19.13810, CaO19.6452
Production host: Escherichia coli / References: UniProt: P28870, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2 M Ammonium Sulfate 0.1 M CAPS/NaOH pH 10.5 0.2 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 15510 / % possible obs: 99 % / Redundancy: 3 % / Net I/σ(I): 20.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
PHENIXdev_1111refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→45.345 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.2
RfactorNum. reflection% reflection
Rfree0.195 1546 9.97 %
Rwork0.18 --
obs0.1815 15510 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.66 Å2 / Biso mean: 42.14 Å2 / Biso min: 27.4 Å2
Refinement stepCycle: final / Resolution: 1.999→45.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 0 161 1960
Biso mean---42.32 -
Num. residues----239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031835
X-RAY DIFFRACTIONf_angle_d0.8842490
X-RAY DIFFRACTIONf_chiral_restr0.048283
X-RAY DIFFRACTIONf_plane_restr0.003326
X-RAY DIFFRACTIONf_dihedral_angle_d13.465686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9991-2.06370.2481280.21141091121987
2.0637-2.13740.21691340.19691273140799
2.1374-2.2230.20051430.195412901433100
2.223-2.32420.22951420.201212901432100
2.3242-2.44670.20931420.196812711413100
2.4467-2.60.21411450.200312801425100
2.6-2.80070.24421380.19931275141399
2.8007-3.08250.22331420.199912781420100
3.0825-3.52840.20371370.18441285142299
3.5284-4.44480.15411490.15241293144299
4.4448-45.35710.17551460.16721338148499

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