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- PDB-1bl4: FKBP MUTANT F36V COMPLEXED WITH REMODELED SYNTHETIC LIGAND -

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Basic information

Entry
Database: PDB / ID: 1bl4
TitleFKBP MUTANT F36V COMPLEXED WITH REMODELED SYNTHETIC LIGAND
ComponentsPROTEIN (FK506 BINDING PROTEIN)
KeywordsISOMERASE / ROTAMASE
Function / homology
Function and homology information


: / extrinsic component of organelle membrane / macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / cytoplasmic side of membrane / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway ...: / extrinsic component of organelle membrane / macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / cytoplasmic side of membrane / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding / regulation of amyloid precursor protein catabolic process / terminal cisterna / signaling receptor inhibitor activity / ryanodine receptor complex / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / regulation of immune response / heart morphogenesis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / protein maturation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / protein folding / regulation of protein localization / protein refolding / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / intracellular membrane-bounded organelle / membrane / cytoplasm / cytosol
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
Chem-AP1 / Peptidyl-prolyl cis-trans isomerase FKBP1A / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHatada, M.H. / Clackson, T. / Yang, W. / Rozamus, L.W. / Amara, J. / Rollins, C.T. / Stevenson, L.F. / Magari, S.R. / Wood, S.A. / Courage, N.L. ...Hatada, M.H. / Clackson, T. / Yang, W. / Rozamus, L.W. / Amara, J. / Rollins, C.T. / Stevenson, L.F. / Magari, S.R. / Wood, S.A. / Courage, N.L. / Lu, X. / Cerasoli Junior, F. / Gilman, M. / Holt, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Redesigning an FKBP-ligand interface to generate chemical dimerizers with novel specificity.
Authors: Clackson, T. / Yang, W. / Rozamus, L.W. / Hatada, M. / Amara, J.F. / Rollins, C.T. / Stevenson, L.F. / Magari, S.R. / Wood, S.A. / Courage, N.L. / Lu, X. / Cerasoli Jr., F. / Gilman, M. / Holt, D.A.
History
DepositionJul 23, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (FK506 BINDING PROTEIN)
B: PROTEIN (FK506 BINDING PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9644
Polymers23,5772
Non-polymers1,3882
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.730, 41.850, 43.590
Angle α, β, γ (deg.)62.61, 82.75, 85.29
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PROTEIN (FK506 BINDING PROTEIN) / FKBP


Mass: 11788.465 Da / Num. of mol.: 2 / Mutation: F36V
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH REDESIGNED COMPOUND / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P62942, UniProt: P20071, peptidylprolyl isomerase
#2: Chemical ChemComp-AP1 / {3-[3-(3,4-DIMETHOXY-PHENYL)-1-(1-{1-[2-(3,4,5-TRIMETHOXY-PHENYL)-BUTYRYL]-PIPERIDIN-2YL}-VINYLOXY)-PROPYL]-PHENOXY}-ACETIC ACID


Mass: 693.780 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H47NO11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.23 Å3/Da / Density % sol: 38 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: VAPOR DIFFUSION IN HANGING DROPS WITH 40 MG/ML COMPLEX AND 1.2M AMMONIUM SULFATE, 0.1M SODIUM PHOSPHATE, PH 6.0 OVER RESERVOIRS OF 2.4 M AMMONIUM SULFATE, vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
21.2 Mammonium sulfate1drop
30.1 Msodium phosphate1drop
420 mMdithiothreitol1drop
52.4 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 15, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 16490 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.16 / % possible all: 91

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FKF

1fkf


Resolution: 1.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1518 10 %RANDOM
Rwork0.188 ---
obs0.188 15095 95 %-
Refine analyze
FreeObs
Luzzati coordinate error0.257 Å0.21 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 100 69 1825
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d1.98
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.25 170 10 %
Rwork0.237 1624 -
obs--94 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.98
LS refinement shell
*PLUS
Rfactor Rfree: 0.25 / % reflection Rfree: 10 % / Rfactor Rwork: 0.237

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