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- PDB-3jym: Crystal Structure of the 3 FKBP domains of wheat FKBP73 -

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Basic information

Entry
Database: PDB / ID: 3jym
TitleCrystal Structure of the 3 FKBP domains of wheat FKBP73
ComponentsFK506-binding protein (FKBP) from wheat
KeywordsISOMERASE / KBP- binding domain five-stranded anti-parallel -sheet and an -helix crossing this sheet / Structural Genomics / Israel Structural Proteomics Center / ISPC
Function / homology
Function and homology information


chaperone-mediated protein folding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calmodulin binding / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / 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 / TPR repeat region circular profile. / TPR repeat profile. ...Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
70 kDa peptidyl-prolyl isomerase
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 2.28 Å
AuthorsDym, O. / Breiman, A. / Israel Structural Proteomics Center (ISPC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2010
Title: Crystal structure of the three FK506 binding protein domains of wheat FKBP73: evidence for a unique wFK73_2 domain
Authors: Unger, T. / Dym, O. / Albeck, S. / Jacobovitch, Y. / Bernehim, R. / Marom, D. / Pisanty, O. / Breiman, A.
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FK506-binding protein (FKBP) from wheat
B: FK506-binding protein (FKBP) from wheat


Theoretical massNumber of molelcules
Total (without water)82,4832
Polymers82,4832
Non-polymers00
Water0
1
A: FK506-binding protein (FKBP) from wheat


Theoretical massNumber of molelcules
Total (without water)41,2421
Polymers41,2421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FK506-binding protein (FKBP) from wheat


Theoretical massNumber of molelcules
Total (without water)41,2421
Polymers41,2421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)186.956, 31.012, 68.978
Angle α, β, γ (deg.)90.00, 93.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FK506-binding protein (FKBP) from wheat


Mass: 41241.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q43207

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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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M NaNitrat 0.1M Bis Tris pH=6.5 20% PEG 3500, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 5, 2007
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.28→46.63 Å / Num. obs: 36745 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.077 / Rsym value: 0.059 / Net I/σ(I): 21
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.36 / Rsym value: 0.433 / % possible all: 95.4

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: PHASER / Resolution: 2.28→46.63 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.828 / SU B: 8.314 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34327 1834 5 %RANDOM
Rwork0.26992 ---
all0.27 35360 --
obs0.27355 34900 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.451 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å2-0.04 Å2
2--1.38 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.28→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 0 0 4726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0224819
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.811.9826498
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1565602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13826.422204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.54615895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6491510
X-RAY DIFFRACTIONr_chiral_restr0.2320.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023552
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2550.22034
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.23088
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6891.53165
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.59724862
X-RAY DIFFRACTIONr_scbond_it431974
X-RAY DIFFRACTIONr_scangle_it5.8814.51636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.279→2.338 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 123 -
Rwork0.294 2444 -
obs--95.29 %

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