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- PDB-3bu1: Crystal structure of monomine-histamine complex -

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Basic information

Entry
Database: PDB / ID: 3bu1
TitleCrystal structure of monomine-histamine complex
ComponentsLipocalin
KeywordsLIGAND BINDING PROTEIN / BETA BARREL / LIPOCALIN
Function / homology
Function and homology information


amine binding / symbiont-mediated perturbation of host defenses
Similarity search - Function
Tick histamine-binding protein / Tick histamine binding protein / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
HISTAMINE / Monomine
Similarity search - Component
Biological speciesArgas monolakensis (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsMans, B.J. / Ribeiro, J.M. / Andersen, J.F.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure, function, and evolution of biogenic amine-binding proteins in soft ticks.
Authors: Mans, B.J. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionDec 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0813
Polymers15,8741
Non-polymers2072
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.418, 56.324, 58.774
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 Lipocalin


Mass: 15874.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Argas monolakensis (arthropod) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q09JX9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HSM / HISTAMINE


Mass: 111.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 1.9 Å3/Da / Density % sol: 35.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2 M Ammonium sulfate, 100 mM Tris HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: SBC-3 / Detector: CCD / Date: Mar 17, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.4→40.66 Å / Num. all: 24335 / Num. obs: 24335 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.046 / Χ2: 0.786 / Net I/σ(I): 10.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 8.2 / Num. unique all: 2293 / Χ2: 0.818 / % possible all: 95.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
EPICS-baseddata aquisition systemdata collection
RefinementResolution: 1.4→40.66 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.707 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 1236 5.1 %RANDOM
Rwork0.151 ---
all0.153 24290 --
obs0.153 24290 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.118 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 13 231 1319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211110
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.9351511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96625.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.07415165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.352154
X-RAY DIFFRACTIONr_chiral_restr0.0650.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02853
X-RAY DIFFRACTIONr_nbd_refined0.1910.2521
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2179
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.238
X-RAY DIFFRACTIONr_mcbond_it0.6511.5717
X-RAY DIFFRACTIONr_mcangle_it1.121137
X-RAY DIFFRACTIONr_scbond_it2.053439
X-RAY DIFFRACTIONr_scangle_it2.6674.5374
X-RAY DIFFRACTIONr_rigid_bond_restr1.5931156
X-RAY DIFFRACTIONr_sphericity_free2.2133231
X-RAY DIFFRACTIONr_sphericity_bonded1.67231088
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.178 83 -
Rwork0.127 1657 -
all-1740 -
obs--98.75 %

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