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- PDB-5htg: Structure of apo P1 form of Candida albicans FKBP12 -

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Basic information

Entry
Database: PDB / ID: 5htg
TitleStructure of apo P1 form of Candida albicans FKBP12
ComponentsFK506-binding protein 1
KeywordsISOMERASE / FKBP12 / pathogenic fungi / calcineurin
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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
DepositionJan 26, 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
Water3,729207
1
A: 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
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)35.899, 38.643, 50.429
Angle α, β, γ (deg.)78.560, 69.670, 79.310
Int Tables number1
Space group name H-MP1

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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.: 207 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: PEG 4000, tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→18 Å / Num. obs: 18999 / % possible obs: 85 % / Redundancy: 1.4 % / Net I/σ(I): 5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→18 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 832 10 %
Rwork0.2168 14687 -
obs0.2205 16318 65.09 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.435 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 86.32 Å2 / Biso mean: 20.0067 Å2 / Biso min: 2.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.1674 Å23.5714 Å22.7549 Å2
2--0.9057 Å20.1792 Å2
3----3.073 Å2
Refinement stepCycle: final / Resolution: 2.4→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 0 207 2049
Biso mean---25.72 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031880
X-RAY DIFFRACTIONf_angle_d0.6582554
X-RAY DIFFRACTIONf_chiral_restr0.037288
X-RAY DIFFRACTIONf_plane_restr0.003338
X-RAY DIFFRACTIONf_dihedral_angle_d13.116708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.47770.32571590.25061376153562
2.4777-2.60820.26941650.21991442160764
2.6082-2.77140.34461570.24731496165365
2.7714-2.98520.24241690.2111471164065
2.9852-3.28510.24351560.21391471162766
3.2851-3.75930.24961700.21451511168168
3.7593-4.7320.1811730.1621565173869
4.732-26.69660.21951790.21511557173669
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)
10.017-0.0671-0.08840.30480.12020.61370.04450.05730.06280.102-0.0544-0.06820.07610.1054-0.06850.0702-0.044-0.03870.1173-0.02060.0834-10.055789.818251.9596
20.1365-0.0437-0.04030.0113-0.02760.16570.0603-0.1056-0.0810.0207-0.0338-0.0047-0.05850.1240.00310.03560.01790.01110.03140.00380.0231-19.766786.008648.2296
30.838-0.04760.15690.63740.19650.48370.21680.1875-0.03220.0859-0.1317-0.13180.0524-0.00770.0420.03640.0169-0.0080.04580.00110.0353-17.470779.454842.4834
40.08230.03840.07190.09670.04750.06340.095-0.10430.12770.0608-0.02380.03450.00080.00890.0020.16550.06550.08580.1090.01630.1052-20.642695.269851.4631
50.1304-0.07290.18860.52880.13730.4184-0.0557-0.02980.00920.1038-0.03250.16170.0301-0.1629-0.08470.0389-0.03670.0129-0.00190.00430.0359-4.037966.275925.3939
60.9090.0126-0.48050.3654-0.14080.57070.0842-0.17060.04970.08120.06090.05950.02530.02930.38710.04360.0097-0.01370.0312-0.01150.051-0.989171.110931.334
70.3237-0.0559-0.05440.07010.02720.103-0.0815-0.0925-0.01-0.15410.0535-0.0308-0.03190.0912-0.00130.1166-0.03270.010.0595-0.00980.08440.515878.313638.7179
80.0356-0.0613-0.0220.28490.00320.0180.07210.0202-0.127-0.0297-0.00560.0096-0.0284-0.01960.02820.11750.0294-0.06570.0804-0.00730.08154.005464.064718.3673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:19)A3 - 19
2X-RAY DIFFRACTION2(chain A and resid 20:80)A20 - 80
3X-RAY DIFFRACTION3(chain A and resid 81:114)A81 - 114
4X-RAY DIFFRACTION4(chain A and resid 115:124)A115 - 124
5X-RAY DIFFRACTION5(chain B and resid 3:30)B3 - 30
6X-RAY DIFFRACTION6(chain B and resid 31:99)B31 - 99
7X-RAY DIFFRACTION7(chain B and resid 100:117)B100 - 117
8X-RAY DIFFRACTION8(chain B and resid 118:124)B118 - 124

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