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- PDB-5hw7: Candida albicans FKBP12 apo protein in P21212 space group -

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Basic information

Entry
Database: PDB / ID: 5hw7
TitleCandida albicans FKBP12 apo protein in P21212 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
FK506-binding protein 1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.291 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


Theoretical massNumber of molelcules
Total (without water)26,1262
Polymers26,1262
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint0 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.813, 80.714, 94.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

21A-237-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.63 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2M Ammonium Sulfate , 0.1M Citrate pH5.5

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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: Nov 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.291→50 Å / Num. obs: 12808 / % possible obs: 98.8 % / Redundancy: 3 % / Biso Wilson estimate: 43.52 Å2 / Rmerge(I) obs: 0.064 / Net I/av σ(I): 23.569 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.291-2.342.20.559192.3
2.34-2.382.60.449195.9
2.38-2.432.70.468198.9
2.43-2.482.90.41199.4
2.48-2.5330.399199.8
2.53-2.593.10.376199.8
2.59-2.663.10.344199.8
2.66-2.733.10.284199.8
2.73-2.813.10.258199.7
2.81-2.93.10.205199.7
2.9-33.10.145199.7
3-3.123.10.121199.8
3.12-3.263.10.1199.7
3.26-3.443.10.077199.7
3.44-3.653.10.062199.7
3.65-3.933.10.05199.8
3.93-4.333.10.038199.8
4.33-4.953.10.029199.4
4.95-6.2430.033198.5
6.24-502.90.025194.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.291→40.905 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.58
RfactorNum. reflection% reflection
Rfree0.2276 1280 10.01 %
Rwork0.1791 --
obs0.1839 12793 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.64 Å2 / Biso mean: 53.43 Å2 / Biso min: 19.99 Å2
Refinement stepCycle: final / Resolution: 2.291→40.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 0 67 1875
Biso mean---47.06 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081846
X-RAY DIFFRACTIONf_angle_d1.4232510
X-RAY DIFFRACTIONf_chiral_restr0.058286
X-RAY DIFFRACTIONf_plane_restr0.009330
X-RAY DIFFRACTIONf_dihedral_angle_d18.146688
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2906-2.38230.35371300.27491164129490
2.3823-2.49070.26221380.24441242138099
2.4907-2.6220.31041400.224212681408100
2.622-2.78620.27141430.221912871430100
2.7862-3.00130.26161420.215312821424100
3.0013-3.30320.28681430.183112791422100
3.3032-3.78090.19991440.176712981442100
3.7809-4.76240.1891470.139513211468100
4.7624-40.91170.1951530.16081372152597
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.68970.44311.24267.46674.18333.90420.0074-0.0849-0.4576-0.16510.17660.41360.2498-0.4889-0.1860.26250.051-0.0360.298-0.00860.6395-0.756791.920434.7233
22.30381.1951-0.42536.0806-0.01213.03980.3114-0.18650.20870.5263-0.20070.3567-0.46960.0457-0.10260.27020.02330.01760.3456-0.04080.32288.705598.866838.1896
35.56713.60520.05625.61560.79272.76370.4895-1.4232-0.01620.6437-0.4421-0.6848-0.13450.20540.00550.39730.0319-0.10950.547-0.03560.493112.176983.345645.309
43.77710.64760.20223.98040.2793.78370.08560.08870.3676-0.2170.0318-0.0978-0.227-0.0523-0.09990.2680.00670.02050.2702-0.00250.32878.432796.308932.4592
54.1113-1.4123-0.84095.25231.26072.5434-0.0395-0.02170.0963-0.2159-0.02730.0522-0.10040.0310.02040.2022-0.01020.0060.24590.03380.19099.107286.382235.9258
69.4926-0.0021-2.91887.813-3.92725.75140.51380.60771.1976-0.1812-0.0355-0.2567-0.5198-0.0274-0.46890.682-0.0510.07040.4236-0.00350.455717.3421104.698710.7333
73.6423-0.01071.23736.434-1.18575.7460.38371.3674-0.0591-1.5412-0.1282-0.34970.4163-0.0699-0.25280.7906-0.06070.04420.6650.03520.498819.419489.64323.7186
82.00141.9887-1.91977.1938-1.72088.6801-0.03780.9801-1.2033-0.3471-0.0342-0.21041.5845-0.34030.04431.07030.0436-0.1360.7876-0.26070.662510.93989.5031-1.3298
93.3566-0.3358-0.67326.1370.42014.48750.10380.21010.31320.04730.08-0.3676-0.62890.2937-0.17390.4718-0.02240.0210.48710.01740.380918.876894.508912.6646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 12 )A3 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 34 )A13 - 34
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 46 )A35 - 46
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 85 )A47 - 85
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 124 )A86 - 124
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 24 )B4 - 24
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 42 )B25 - 42
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 49 )B43 - 49
9X-RAY DIFFRACTION9chain 'B' and (resid 50 through 122 )B50 - 122

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