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- PDB-2ppo: Crystal structure of E60A mutant of FKBP12 -

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Basic information

Entry
Database: PDB / ID: 2ppo
TitleCrystal structure of E60A mutant of FKBP12
ComponentsFK506-binding protein 1A
KeywordsLYASE / high resolution protein structure
Function / homology
Function and homology information


macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / 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 ...macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / 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 / signaling receptor inhibitor activity / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / calcium channel regulator activity / protein maturation / T cell activation / peptidyl-prolyl cis-trans isomerase activity / sarcoplasmic reticulum / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / 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 / membrane / cytosol / cytoplasm
Similarity search - Function
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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsSzep, S. / Park, S. / VanDuyne, G.D. / Saven, J.G.
CitationJournal: Proteins / Year: 2009
Title: Structural coupling between FKBP12 and buried water.
Authors: Szep, S. / Park, S. / Boder, E.T. / Van Duyne, G.D. / Saven, J.G.
History
DepositionApr 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FK506-binding protein 1A


Theoretical massNumber of molelcules
Total (without water)11,7781
Polymers11,7781
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.793, 62.563, 32.420
Angle α, β, γ (deg.)90.00, 113.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FK506-binding protein 1A / Peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase / 12 kDa FKBP / FKBP-12 / Immunophilin FKBP12


Mass: 11778.472 Da / Num. of mol.: 1 / Mutation: E61A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.9-2.1 M Sodium Maleonate, 50 mM DMSO, Slow buffer exchange into 2.5 M Sodium Maleoneate no DMSO, in 10 minute steps for freezing, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.29→25 Å / Num. all: 31805 / Num. obs: 29420 / % possible obs: 92.5 % / Observed criterion σ(F): 17.63 / Observed criterion σ(I): 46.2 / Redundancy: 3.5 % / Biso Wilson estimate: 14.14 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 46.2
Reflection shellResolution: 1.29→1.35 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / Num. unique all: 1848 / Rsym value: 0.32 / % possible all: 80.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native fkbp structure solved in this study

Resolution: 1.29→25 Å / Cross valid method: THROUGHOUT / σ(I): 2.75 / Stereochemistry target values: Engh & Huber / Details: used anisotropic B factor refinement in Shelx
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 1471 -random
Rwork0.1329 ---
all0.1885 31805 --
obs0.1888 29420 92.5 %-
Displacement parametersBiso mean: 13.94 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å2-0.02 Å2
2--0 Å2-0.02 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.29→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms869 0 0 137 1006
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d1.205
X-RAY DIFFRACTIONs_bond_d0.007
LS refinement shellResolution: 1.29→1.35 Å /
Num. reflection% reflection
Rfree132 -
obs2651 80.4 %

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