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- PDB-5i7q: Crystal structure of Fkbp12-IF(SlpA), a chimeric protein of human... -

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Basic information

Entry
Database: PDB / ID: 5i7q
TitleCrystal structure of Fkbp12-IF(SlpA), a chimeric protein of human Fkbp12 and the insert in flap domain of Ecoli SlpA
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A,FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase,Peptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / Fkbp12 / prolyl isomerization / chaperone / SlyD / "insert in flap" / chimeric protein / protein design / SlpA / PPIase
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 / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / signaling receptor inhibitor activity / '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 / supramolecular fiber organization / : / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / protein maturation / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / SARS-CoV-1 activates/modulates innate immune responses / Z disc / 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
Thrombin, subunit H - #330 / : / 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 / Thrombin, subunit H ...Thrombin, subunit H - #330 / : / 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 / Thrombin, subunit H / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJakob, R.P. / Dobbek, H. / Schmid, F.X.
CitationJournal: To Be Published
Title: Structural and Functional Analysis of Chaperone Domain Insertion in Fkbp12
Authors: Zoldak, G. / Knappe, T.A. / Geitner, A.-J. / Scholz, C. / Dobbek, H. / Schmid, F.X. / Jakob, R.P.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP1A,FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase,Peptidyl-prolyl cis-trans isomerase FKBP1A


Theoretical massNumber of molelcules
Total (without water)18,1231
Polymers18,1231
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.840, 63.610, 46.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A,FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase,Peptidyl-prolyl cis-trans isomerase FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / ...PPIase FKBP1A / 12 kDa FK506-binding protein / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase / PPIase / Rotamase / PPIase FKBP1A / 12 kDa FK506-binding protein / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 18123.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: FKBP1A, FKBP1, FKBP12, fkpB, slpA, yaaD, b0028, JW0026
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P62942, UniProt: P0AEM0, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25 % PEG1500, 10 % isopropanol, 0.1 M CaCl2, 0.1 M Mes pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25.18 Å / Num. obs: 12984 / % possible obs: 96.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.144 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2131: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fkk

1fkk


Resolution: 1.9→25.18 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.12
RfactorNum. reflection% reflection
Rfree0.2383 756 5.82 %
Rwork0.2033 --
obs0.2053 12984 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→25.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 0 258 1471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051251
X-RAY DIFFRACTIONf_angle_d0.6831689
X-RAY DIFFRACTIONf_dihedral_angle_d10.402760
X-RAY DIFFRACTIONf_chiral_restr0.05180
X-RAY DIFFRACTIONf_plane_restr0.004225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9002-2.04680.30351520.28882405X-RAY DIFFRACTION97
2.0468-2.25270.27551660.23822356X-RAY DIFFRACTION96
2.2527-2.57840.26531410.242393X-RAY DIFFRACTION96
2.5784-3.24740.23761380.1922536X-RAY DIFFRACTION100
3.2474-25.18240.19011590.15412538X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.80990.2383-0.25471.88520.3610.5221-0.07120.1114-0.04140.2429-0.12860.22720.1987-0.2153-0.03790.0688-0.02570.03330.06450.01540.236335.6141-7.587724.319
21.7154-0.2111-0.70912.45220.17231.8470.10070.0588-0.0307-0.04380.1016-0.0818-0.21180.0732-0.00980.0071-0.0144-0.02990.0220.00160.10448.7102-1.940718.4272
31.3622-0.24440.00381.631-0.32621.20910.03610.14080.04270.04530.0790.3817-0.0604-0.1835-0.04790.0318-0.0011-0.00240.06570.0120.151639.00831.095716.964
46.56692.11330.44361.96130.74642.2420.15710.66450.4528-0.27330.33770.3923-0.0049-0.05120.34380.1838-0.0131-0.06230.14750.12630.252857.871325.18966.3847
53.93341.07360.76353.3324-0.37581.3349-0.2641-0.1731-0.3911-0.12290.24490.11740.0149-0.0202-0.10020.0979-0.02360.05260.06320.01790.194463.103719.429312.5109
64.38360.8626-2.81554.8067-1.43415.1748-0.23940.3793-0.3815-0.51830.42230.55560.0318-0.48680.02240.185-0.04030.0310.16390.05390.193658.783417.98876.8529
70.8860.682-0.09211.05840.3860.2582-0.0390.16720.1290.09390.12010.103-0.14920.0223-0.03830.0791-0.0176-0.02710.08720.04940.138849.20275.952813.4505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 118 )
6X-RAY DIFFRACTION6chain 'A' and (resid 119 through 128 )
7X-RAY DIFFRACTION7chain 'A' and (resid 129 through 156 )

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