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- PDB-5ht1: Structure of apo C. glabrata FKBP12 -

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Basic information

Entry
Database: PDB / ID: 5ht1
TitleStructure of apo C. glabrata FKBP12
ComponentsFK506-binding protein 1
KeywordsISOMERASE / FKBP12 / C. glabrata / pahtogenesis
Function / homology
Function and homology information


negative regulation of homoserine biosynthetic process / : / 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 / 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 glabrata (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.651 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

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Assembly

Deposited unit
A: FK506-binding protein 1


Theoretical massNumber of molelcules
Total (without water)12,2411
Polymers12,2411
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.436, 76.436, 87.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 12240.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus)
Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65
Gene: FPR1, CAGL0K09724g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FMA3, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, 0.1 M Tris 7.5

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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: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→43.508 Å / Num. obs: 3991 / % possible obs: 99.99 % / Redundancy: 3.3 % / Net I/σ(I): 11.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.651→43.508 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2627 399 10 %
Rwork0.1912 --
obs0.1984 3991 99.92 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.584 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.609 Å20 Å2-0 Å2
2--3.609 Å20 Å2
3----7.218 Å2
Refinement stepCycle: LAST / Resolution: 2.651→43.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 0 20 881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008881
X-RAY DIFFRACTIONf_angle_d1.1831195
X-RAY DIFFRACTIONf_dihedral_angle_d15.544328
X-RAY DIFFRACTIONf_chiral_restr0.075131
X-RAY DIFFRACTIONf_plane_restr0.005158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6507-3.03420.33721300.24671166X-RAY DIFFRACTION100
3.0342-3.82240.24931300.19041174X-RAY DIFFRACTION100
3.8224-43.51430.24191390.16991252X-RAY DIFFRACTION100

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