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- PDB-2ppp: Crystal structure of E60Q mutant of FKBP12 -

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Basic information

Entry
Database: PDB / ID: 2ppp
TitleCrystal structure of E60Q mutant of FKBP12
ComponentsFK506-binding protein 1A
KeywordsLYASE / high resolution protein structure
Function / homology
Function and homology information


macrolide binding / activin receptor binding / cytoplasmic side of membrane / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / signaling receptor inhibitor activity / 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 ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / signaling receptor inhibitor activity / 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 / terminal cisterna / ryanodine receptor complex / I-SMAD binding / regulation of amyloid precursor protein catabolic process / protein maturation by protein folding / ventricular cardiac muscle tissue morphogenesis / 'de novo' protein folding / FK506 binding / channel regulator activity / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / negative regulation of transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / Z disc / regulation of protein localization / SARS-CoV-1 activates/modulates innate immune responses / protein folding / positive regulation of protein binding / positive regulation of canonical NF-kappaB signal transduction / protein refolding / Potential therapeutics for SARS / transmembrane transporter binding / amyloid fibril formation / membrane / cytoplasm / cytosol
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 domain / FKBP-type peptidyl-prolyl cis-trans isomerase / 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: 0.94 Å
AuthorsSzep, S. / Park, S. / VanDuyne, G.D. / Saven, J.F.
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 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 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)11,8361
Polymers11,8361
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.602, 62.517, 32.248
Angle α, β, γ (deg.)90.00, 114.14, 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: 11835.522 Da / Num. of mol.: 1 / Mutation: E61Q
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.: 123 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
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: 1.04 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: 1.04 Å / Relative weight: 1
ReflectionResolution: 0.94→50 Å / Num. all: 66832 / Num. obs: 62089 / % possible obs: 89.5 % / Observed criterion σ(F): 32.11 / Observed criterion σ(I): 24.7 / Redundancy: 3.3 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 24.7
Reflection shellResolution: 0.94→1.01 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.75 / Rsym value: 0.287 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CCP4model building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: fkbp native structure solved in this study

Resolution: 0.94→31.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.339 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22002 3136 5.1 %RANDOM
Rwork0.20259 ---
obs0.20345 58921 92.86 %-
all-66832 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.317 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.124 Å
Refinement stepCycle: LAST / Resolution: 0.94→31.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 0 123 1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.961425
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68823.67349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45215192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.526159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02850
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.2428
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2704
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6731.5670
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06321060
X-RAY DIFFRACTIONr_scbond_it1.3523420
X-RAY DIFFRACTIONr_scangle_it1.9044.5365
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.94→0.966 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 98 -
Rwork0.312 1708 -
obs--36.55 %

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