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- PDB-5hw6: Candida albicans FKBP12 apo protein in C2 space group -

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Basic information

Entry
Database: PDB / ID: 5hw6
TitleCandida albicans FKBP12 apo protein in C2 space group
ComponentsFK506-binding protein 1
KeywordsISOMERASE / FKBP12 / prolyl isomerase
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
ACETATE ION / FK506-binding protein 1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsTonthat, N.K. / Schumacher, 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
DepositionJan 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1853
Polymers26,1262
Non-polymers591
Water2,324129
1
A: FK506-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1222
Polymers13,0631
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FK506-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,0631
Polymers13,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.474, 42.980, 70.696
Angle α, β, γ (deg.)90.000, 128.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13062.796 Da / Num. of mol.: 2
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 (E. coli) / References: UniProt: P28870, peptidylprolyl isomerase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 8000, 0.1 M Sodium acetate pH 4.5 and 0.2M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Mar 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 9189 / % possible obs: 98.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.101 / Χ2: 1.373 / Net I/av σ(I): 13.152 / Net I/σ(I): 13.1 / Num. measured all: 30224
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.442.40.197193.8
2.44-2.492.60.206196
2.49-2.532.70.206194.4
2.53-2.592.70.181197.3
2.59-2.642.80.184196.4
2.64-2.730.181196.8
2.7-2.7730.172198
2.77-2.853.20.168197.9
2.85-2.933.30.147199.1
2.93-3.023.40.135199.4
3.02-3.133.50.119199.4
3.13-3.263.60.11199.1
3.26-3.413.70.1011100
3.41-3.583.70.091199.8
3.58-3.813.70.096199.8
3.81-4.13.70.086199.8
4.1-4.523.70.0821100
4.52-5.173.70.0791100
5.17-6.513.60.084199.6
6.51-503.40.067197.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.401→25.96 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.21 / Phase error: 20.74
RfactorNum. reflection% reflection
Rfree0.2221 884 10.02 %
Rwork0.1774 --
obs0.1818 8825 94.34 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Bsol: 39.451 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso max: 67.41 Å2 / Biso mean: 24.5815 Å2 / Biso min: 1.96 Å2
Baniso -1Baniso -2Baniso -3
1--2.5051 Å20 Å2-0.9613 Å2
2--3.6115 Å20 Å2
3----1.1064 Å2
Refinement stepCycle: final / Resolution: 2.401→25.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 7 129 1869
Biso mean--59.08 27.8 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031773
X-RAY DIFFRACTIONf_angle_d0.8612417
X-RAY DIFFRACTIONf_chiral_restr0.047280
X-RAY DIFFRACTIONf_plane_restr0.003317
X-RAY DIFFRACTIONf_dihedral_angle_d11.648644
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4014-2.55170.27191370.19131232136989
2.5517-2.74850.23181390.18471254139391
2.7485-3.02470.24341480.18381331147995
3.0247-3.46150.20021480.1721331147996
3.4615-4.35780.20641530.15951383153698
4.3578-25.96120.21871590.18741410156997
Refinement TLS params.Method: refined / Origin x: 38.1895 Å / Origin y: -34.8848 Å / Origin z: 14.1222 Å
111213212223313233
T0.0981 Å2-0.0133 Å20.0007 Å2-0.0704 Å20.0153 Å2--0.1016 Å2
L0.3255 °20.1309 °2-0.1161 °2--0.0594 °20.2622 °2--0.296 °2
S0.0177 Å °-0.0302 Å °0.0026 Å °0.0167 Å °-0.0005 Å °-0.0045 Å °-0.013 Å °-0.0116 Å °0.0267 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 122
2X-RAY DIFFRACTION1allB3 - 122
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 129

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