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

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Basic information

Entry
Database: PDB / ID: 3aos
TitleCrystal structure of juvenile hormone binding protein from silkworm in complex with JH II
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
Chem-JH2 / 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
B: Hemolymph juvenile hormone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1234
Polymers49,5622
Non-polymers5612
Water2,234124
1
A: Hemolymph juvenile hormone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0612
Polymers24,7811
Non-polymers2801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemolymph juvenile hormone binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0612
Polymers24,7811
Non-polymers2801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.044, 46.750, 72.169
Angle α, β, γ (deg.)90.00, 102.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemolymph juvenile hormone binding protein


Mass: 24781.092 Da / Num. of mol.: 2 / 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-JH2 / methyl (2E,6E)-9-[(2R,3S)-3-ethyl-3-methyloxiran-2-yl]-3,7-dimethylnona-2,6-dienoate / JH II, Juvenile hormone II


Mass: 280.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H28O3 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 15% PEG 3350, 0.05M zinc acetate, 0.1M sodium citrate, pH 4.2, 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: Oct 22, 2009
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: 24811 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 20.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1826 / % possible all: 68.1

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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 3A1Z

3a1z


Resolution: 2.2→29.95 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.455 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29076 1232 5 %RANDOM
Rwork0.23918 ---
obs0.24172 23565 90.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.441 Å2
Baniso -1Baniso -2Baniso -3
1--2.75 Å20 Å20.44 Å2
2---2.9 Å20 Å2
3---5.84 Å2
Refine analyzeLuzzati coordinate error obs: 0.5467 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3404 0 40 124 3568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.631.994751
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.42326.454141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.63715629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.811158
X-RAY DIFFRACTIONr_chiral_restr0.1110.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212556
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_it0.7811.52211
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43923594
X-RAY DIFFRACTIONr_scbond_it2.12731291
X-RAY DIFFRACTIONr_scangle_it3.4654.51151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.204→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 52 -
Rwork0.236 1270 -
obs--66.2 %

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