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- PDB-3aot: Crystal structure of juvenile hormone binding protein from silkwo... -

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Basic information

Entry
Database: PDB / ID: 3aot
TitleCrystal structure of juvenile hormone binding protein from silkworm in its apo form
ComponentsHemolymph juvenile hormone binding protein
KeywordsHormone binding protein / Beta-barrel / juvenile hormone / Hemolymph
Function / homology
Function and homology information


TULIP domain / Haemolymph juvenile hormone binding / Takeout superfamily / Haemolymph juvenile hormone binding protein (JHBP) / Juvenile hormone binding protein domains in insects. / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Hemolymph juvenile hormone binding protein
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFujimoto, Z. / Suzuki, R. / Shiotsuki, T. / Momma, M. / Yamazaki, T.
Citation
Journal: Sci Rep / Year: 2011
Title: Structural mechanism of JH delivery in hemolymph by JHBP of silkworm, Bombyx mori.
Authors: Suzuki, R. / Fujimoto, Z. / Shiotsuki, T. / Tsuchiya, W. / Momma, M. / Tase, A. / Miyazawa, M. / Yamazaki, T.
#1: Journal: Biomol.Nmr Assign. / Year: 2009
Title: NMR assignments of juvenile hormone binding protein in complex with JH III
Authors: Suzuki, R. / Tase, A. / Fujimoto, Z. / Shiotsuki, T. / Yamazaki, T.
History
DepositionOct 6, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 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_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 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemolymph juvenile hormone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,22110
Polymers24,7811
Non-polymers1,4409
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.898, 90.898, 138.336
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Hemolymph juvenile hormone binding protein


Mass: 24781.092 Da / Num. of mol.: 1 / Fragment: UNP residues 19-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: hJHBP / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9U556
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50% PEG 200, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 19, 2010
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17925 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 20.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 57.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 11.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AOS

3aos


Resolution: 2.2→37.86 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.509 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25453 905 5.1 %RANDOM
Rwork0.23416 ---
obs0.23515 16943 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.982 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.39 Å20 Å2
2--0.77 Å20 Å2
3----1.16 Å2
Refine analyzeLuzzati coordinate error obs: 0.1233 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 96 51 1706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221672
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5792.0082230
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.47126.30865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41215284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.218154
X-RAY DIFFRACTIONr_chiral_restr0.1120.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211161
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1391.51013
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.10221650
X-RAY DIFFRACTIONr_scbond_it2.6183659
X-RAY DIFFRACTIONr_scangle_it4.44.5580
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.197→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 70 -
Rwork0.22 1211 -
obs--99.46 %

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