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- PDB-4it4: Crystal structure of residues 1-211 of CG17282 -

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Basic information

Entry
Database: PDB / ID: 4it4
TitleCrystal structure of residues 1-211 of CG17282
ComponentsCG17282
KeywordsUNKNOWN FUNCTION / Immunophilin
Function / homology
Function and homology information


regulation of post-translational protein modification / regulation of establishment of planar polarity / kinase activator activity / regulation of protein catabolic process / regulation of intracellular protein transport / locomotor rhythm / cytosol
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #320 / BDBT FKBP like, N-terminal / : / BDBT FKBP like N-terminal / Bride of doubletime-like, TPR domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Elongation Factor Tu (Ef-tu); domain 3 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Tetratricopeptide-like helical domain superfamily / Up-down Bundle ...Elongation Factor Tu (Ef-tu); domain 3 - #320 / BDBT FKBP like, N-terminal / : / BDBT FKBP like N-terminal / Bride of doubletime-like, TPR domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Elongation Factor Tu (Ef-tu); domain 3 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / FORMIC ACID / Protein Bride of doubletime
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAgyekum, B. / Bouyain, S.
CitationJournal: Neuron / Year: 2013
Title: Noncanonical FK506-Binding Protein BDBT Binds DBT to Enhance Its Circadian Function and Forms Foci at Night.
Authors: Fan, J.Y. / Agyekum, B. / Venkatesan, A. / Hall, D.R. / Keightley, A. / Bjes, E.S. / Bouyain, S. / Price, J.L.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG17282
B: CG17282
C: CG17282
D: CG17282
E: CG17282
F: CG17282
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,41820
Polymers145,5296
Non-polymers88914
Water2,072115
1
A: CG17282
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3473
Polymers24,2551
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CG17282
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4854
Polymers24,2551
Non-polymers2303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CG17282
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4393
Polymers24,2551
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CG17282
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3473
Polymers24,2551
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: CG17282
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3012
Polymers24,2551
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: CG17282
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4995
Polymers24,2551
Non-polymers2444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16650 Å2
ΔGint-71 kcal/mol
Surface area56520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.098, 90.193, 249.671
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CG17282 / RE50353p


Mass: 24254.889 Da / Num. of mol.: 6 / Fragment: UNP Residues 1-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG17282, Dmel_CG17282 / Plasmid: pT7HMP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VDE4
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 8% (v/v) Tacsimate pH 4.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2012
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 99606 / Num. obs: 53197 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.129 / Χ2: 1.037 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.594.30.69552281.165199.7
2.59-2.695.40.67752141.264199.8
2.69-2.826.70.5652490.9981100
2.82-2.9680.48552581.0891100
2.96-3.158.60.34352891.1091100
3.15-3.398.70.22352750.9961100
3.39-3.738.60.16753101.0091100
3.73-4.278.50.13553400.9881100
4.27-5.388.30.09954030.9621100
5.38-507.80.09556310.954199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Residues 1-120 of CG17282

Resolution: 2.5→39.65 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8017 / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 2513 4.98 %RANDOM
Rwork0.1971 ---
all0.1987 52929 --
obs0.1987 50416 94.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.91 Å2 / Biso mean: 56.5659 Å2 / Biso min: 21.99 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9870 0 58 115 10043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810092
X-RAY DIFFRACTIONf_angle_d0.96213587
X-RAY DIFFRACTIONf_chiral_restr0.0631568
X-RAY DIFFRACTIONf_plane_restr0.0041681
X-RAY DIFFRACTIONf_dihedral_angle_d16.4273766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.53510.41111160.32187230378
2.5351-2.58690.32751260.2712382250887
2.5869-2.64310.33231300.26872450258088
2.6431-2.70460.33951280.26292497262590
2.7046-2.77220.26281360.25192549268591
2.7722-2.84710.30271310.25042512264391
2.8471-2.93090.28991310.24852542267391
2.9309-3.02550.28311360.25692654279094
3.0255-3.13360.3181380.2492653279196
3.1336-3.2590.3021420.2412722286497
3.259-3.40720.25481450.21862750289598
3.4072-3.58670.2291450.20432771291699
3.5867-3.81130.24661470.18812807295499
3.8113-4.10530.18111490.17812826297599
4.1053-4.51790.19371500.159728162966100
4.5179-5.17040.20031500.156228683018100
5.1704-6.50950.22161530.199128963049100
6.5095-39.650.19871600.1823021318199

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