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- PDB-5d75: Crystal structure of Human FKBD25 in complex with FK506 -

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Basic information

Entry
Database: PDB / ID: 5d75
TitleCrystal structure of Human FKBD25 in complex with FK506
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP3
KeywordsISOMERASE/INHIBITOR / FK506 / FKBP25 / FKBP3 / Immunophilin / Inhibitor / ISOMERASE-INHIBITOR complex
Function / homology
Function and homology information


FK506 binding / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / signaling receptor activity / RNA binding / nucleus
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase FKBP3 / FKBP3, basic tilted helix bundle domain / Basic tilted helix bundle domain / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / Chem-JEF / Peptidyl-prolyl cis-trans isomerase FKBP3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsRajan, S. / Prakash, A. / Yoon, H.S.
CitationJournal: Protein Sci. / Year: 2016
Title: Crystal structure of the FK506 binding domain of human FKBP25 in complex with FK506.
Authors: Prakash, A. / Rajan, S. / Yoon, H.S.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 2.0Oct 3, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_oper_list.symmetry_operation / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Peptidyl-prolyl cis-trans isomerase FKBP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0314
Polymers14,0311
Non-polymers2,0003
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.784, 74.784, 44.618
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

21A-506-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP3 / PPIase FKBP3 / 25 kDa FK506-binding protein / FKBP-25 / FK506-binding protein 3 / FKBP-3 / ...PPIase FKBP3 / 25 kDa FK506-binding protein / FKBP-25 / FK506-binding protein 3 / FKBP-3 / Immunophilin FKBP25 / Rapamycin-selective 25 kDa immunophilin / Rotamase


Mass: 14031.117 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 109-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP3, FKBP25 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q00688, peptidylprolyl isomerase
#2: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506


Mass: 804.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H69NO12 / Comment: medication*YM
#3: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H63NO10
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% v/v Jeffamine ED-2001, 0.1M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. obs: 12952 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 34.4
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBK

1pbk


Resolution: 1.83→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.193 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23311 1025 8.1 %RANDOM
Rwork0.187 ---
obs0.19073 11605 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.411 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.83→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 91 106 1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021063
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5492.051423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0795119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01425.52638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89115187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.924152
X-RAY DIFFRACTIONr_chiral_restr0.0990.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021732
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8032.145479
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.173.207597
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2012.533582
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.35518.9011605
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.831→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 60 -
Rwork0.26 594 -
obs--68.2 %

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