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- PDB-4ipx: Analyzing the visible conformational substates of the FK506 bindi... -

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Basic information

Entry
Database: PDB / ID: 4ipx
TitleAnalyzing the visible conformational substates of the FK506 binding protein FKBP12
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE
Function / homology
Function and homology information


macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / regulation of amyloid precursor protein catabolic process / heart trabecula formation ...macrolide binding / activin receptor binding / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / regulation of amyloid precursor protein catabolic process / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / protein maturation by protein folding / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / negative regulation of phosphoprotein phosphatase activity / FK506 binding / mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / regulation of immune response / protein peptidyl-prolyl isomerization / supramolecular fiber organization / heart morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / T cell activation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / protein folding / positive regulation of protein binding / protein refolding / positive regulation of canonical NF-kappaB signal transduction / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / 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 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChen, H. / Mustafi, S.M. / Li, H.M. / LeMaster, D.M. / Hernandez, G.
CitationJournal: Biochem.J. / Year: 2013
Title: Analysing the visible conformational substates of the FK506-binding protein FKBP12.
Authors: Mustafi, S.M. / Chen, H. / Li, H. / Lemaster, D.M. / Hernandez, G.
History
DepositionJan 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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 FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0303
Polymers11,7931
Non-polymers2362
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.550, 35.948, 40.923
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-409-

HOH

31A-410-

HOH

41A-411-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding ...PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 11793.480 Da / Num. of mol.: 1 / Mutation: C22V, H87V
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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.7 M sodium malonate, pH 7.0, 0.1 M HEPES, pH 7.4, 5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 28, 2012
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. obs: 10996 / % possible obs: 93.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.23 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 29.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 6.3 / Rsym value: 0.296 / % possible all: 93.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PPN

2ppn


Resolution: 1.7→19.607 Å / SU ML: 0.31 / σ(F): 1.55 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 543 4.94 %
Rwork0.2067 --
obs0.2072 10991 96.64 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.491 Å2 / ksol: 0.421 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.361 Å20 Å2-1.5648 Å2
2--6.1164 Å20 Å2
3----1.7554 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 16 127 973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006862
X-RAY DIFFRACTIONf_angle_d1.1111165
X-RAY DIFFRACTIONf_dihedral_angle_d14.809325
X-RAY DIFFRACTIONf_chiral_restr0.069126
X-RAY DIFFRACTIONf_plane_restr0.005150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.8710.40381420.36292512X-RAY DIFFRACTION95
1.871-2.14140.22751370.18652583X-RAY DIFFRACTION96
2.1414-2.69680.19681240.18192650X-RAY DIFFRACTION98
2.6968-19.60790.19161400.19942703X-RAY DIFFRACTION98

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