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- PDB-3uqi: Crystallographic structure of FKBP12 from Aedes aegypti -

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Basic information

Entry
Database: PDB / ID: 3uqi
TitleCrystallographic structure of FKBP12 from Aedes aegypti
ComponentsFKBP-type peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / FKBP12 / FK506 Binding
Function / homology
Function and homology information


sarcoplasmic reticulum membrane / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
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 / Roll / Alpha Beta
Similarity search - Domain/homology
peptidylprolyl isomerase
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.302 Å
AuthorsSreekanth, R. / Saw, K.Q. / Yoon, H.S.
CitationJournal: Protein Sci. / Year: 2012
Title: High-resolution crystal structure of FKBP12 from Aedes aegypti.
Authors: Rajan, S. / Saw, K.Q. / Nguyen, Q.T. / Baek, K. / Yoon, H.S.
History
DepositionNov 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: FKBP-type peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8583
Polymers11,5531
Non-polymers3052
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.826, 38.677, 79.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP12 / Fk506-binding protein


Mass: 11553.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: AAEL007883, AaeL_AAEL007883 / Plasmid: pETSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1HR83, peptidylprolyl isomerase
#2: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM MOPS pH 8.0, 3.0M Ammonium Sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 23141 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 14.89 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 54.7
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2228 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PPN

2ppn


Resolution: 1.302→23.867 Å / SU ML: 0.29 / σ(F): 1.37 / Phase error: 16.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1903 1184 5.15 %
Rwork0.1631 --
obs0.1643 23012 98.83 %
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.578 Å2 / ksol: 0.428 e/Å3
Displacement parametersBiso mean: 23.8499 Å2
Baniso -1Baniso -2Baniso -3
1--2.789 Å20 Å2-0 Å2
2--2.5051 Å20 Å2
3---0.2839 Å2
Refinement stepCycle: LAST / Resolution: 1.302→23.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 18 131 962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013848
X-RAY DIFFRACTIONf_angle_d1.5561151
X-RAY DIFFRACTIONf_dihedral_angle_d15.409310
X-RAY DIFFRACTIONf_chiral_restr0.112125
X-RAY DIFFRACTIONf_plane_restr0.011149
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3018-1.3610.28461520.23612560271295
1.361-1.43280.26231580.18872663282198
1.4328-1.52250.25751460.16712675282199
1.5225-1.640.19521480.15472725287399
1.64-1.8050.21571460.146727352881100
1.805-2.06610.13651400.142827492889100
2.0661-2.60260.19831580.141827882946100
2.6026-23.87050.1751360.175829333069100

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