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- PDB-3b7x: Crystal structure of human FK506-Binding Protein 6 -

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Basic information

Entry
Database: PDB / ID: 3b7x
TitleCrystal structure of human FK506-Binding Protein 6
ComponentsFK506-binding protein 6
KeywordsISOMERASE / Rotamase / TPR repeat / Williams-Beuren syndrome / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by siRNA-mediated heterochromatin formation / piRNA processing / synaptonemal complex / regulatory ncRNA-mediated gene silencing / FK506 binding / PIWI-interacting RNA (piRNA) biogenesis / positive regulation of viral genome replication / Meiotic synapsis / meiotic cell cycle ...transposable element silencing by piRNA-mediated DNA methylation / transposable element silencing by siRNA-mediated heterochromatin formation / piRNA processing / synaptonemal complex / regulatory ncRNA-mediated gene silencing / FK506 binding / PIWI-interacting RNA (piRNA) biogenesis / positive regulation of viral genome replication / Meiotic synapsis / meiotic cell cycle / Hsp90 protein binding / protein folding / spermatogenesis / cell differentiation / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Inactive peptidyl-prolyl cis-trans isomerase FKBP6/shutdown / 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 / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...Inactive peptidyl-prolyl cis-trans isomerase FKBP6/shutdown / 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 / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Inactive peptidyl-prolyl cis-trans isomerase FKBP6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalker, J.R. / Davis, T. / Butler-Cole, C. / Paramanathan, R. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human FK506-Binding Protein 6.
Authors: Walker, J.R. / Davis, T. / Butler-Cole, C. / Paramanathan, R. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionOct 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FK506-binding protein 6


Theoretical massNumber of molelcules
Total (without water)15,0741
Polymers15,0741
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.059, 55.059, 229.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein FK506-binding protein 6 / Peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase / 36 kDa FK506-binding protein / FKBP-36 / ...Peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase / 36 kDa FK506-binding protein / FKBP-36 / Immunophilin FKBP36


Mass: 15074.242 Da / Num. of mol.: 1 / Fragment: PPIase FKBP-Type Domain: Residues 12-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP6, FKBP36 / Plasmid: p28a-mhl / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75344, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Mixed equal volumes of 1.6M MgSO4, 0.1M MES pH 6.5, and 10 mg/mL protein. Crystals were cryoprotected by transferring the crystals to a drop containing mother liquor to which glycerol was ...Details: Mixed equal volumes of 1.6M MgSO4, 0.1M MES pH 6.5, and 10 mg/mL protein. Crystals were cryoprotected by transferring the crystals to a drop containing mother liquor to which glycerol was added to a final concentration of 20%, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 10831 / Num. obs: 10831 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rsym value: 0.054 / Net I/σ(I): 46.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 6.7 / Num. unique all: 1037 / Rsym value: 0.365 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KT0

1kt0


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.637 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28215 549 5.1 %RANDOM
Rwork0.25643 ---
obs0.2577 10261 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.575 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å20 Å20 Å2
2--3.41 Å20 Å2
3----6.83 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 0 55 977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022939
X-RAY DIFFRACTIONr_angle_refined_deg1.4892.0121268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8435114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57123.33342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.58315163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.694158
X-RAY DIFFRACTIONr_chiral_restr0.1080.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02703
X-RAY DIFFRACTIONr_nbd_refined0.210.2401
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.211
X-RAY DIFFRACTIONr_mcbond_it0.841.5598
X-RAY DIFFRACTIONr_mcangle_it1.4812925
X-RAY DIFFRACTIONr_scbond_it1.8833389
X-RAY DIFFRACTIONr_scangle_it3.0214.5343
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 46 -
Rwork0.3 722 -
obs--96.97 %

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