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- PDB-3bu9: Selenomethionine derivative of monomine L57,63,87,146M mutant -

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Basic information

Entry
Database: PDB / ID: 3bu9
TitleSelenomethionine derivative of monomine L57,63,87,146M mutant
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
Biological speciesArgas monolakensis (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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
DepositionJan 2, 2008Deposition 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 1.3Oct 9, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipocalin


Theoretical massNumber of molelcules
Total (without water)16,1811
Polymers16,1811
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.281, 56.547, 58.747
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: 16180.850 Da / Num. of mol.: 1 / Mutation: L57,63,87,146M mutant
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.86 Å3/Da / Density % sol: 33.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2M 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: 0.97918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2007 / Details: Si(111)
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionRedundancy: 3.9 % / Av σ(I) over netI: 11.2 / Number: 181485 / Rmerge(I) obs: 0.05 / Χ2: 0.99 / D res high: 1.4 Å / D res low: 20 Å / Num. obs: 45974 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.012099.710.0271.1554
2.393.0110010.0381.3054
2.092.3910010.0441.1444.1
1.92.0910010.0611.2514.1
1.761.910010.0790.8514.1
1.661.7610010.1130.8024
1.581.6610010.1460.7914
1.511.5810010.20.8814
1.451.5110010.2510.8733.9
1.41.4510010.3110.8453.5
ReflectionResolution: 1.4→40.76 Å / Num. all: 45974 / Num. obs: 45974 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Χ2: 0.993 / Net I/σ(I): 11.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4575 / Χ2: 0.845 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.4 Å / D res low: 15 Å / FOM : 0.314 / FOM acentric: 0.356 / FOM centric: 0 / Reflection: 24406 / Reflection acentric: 21483 / Reflection centric: 2923
Phasing MAD setR cullis acentric: 2 / R cullis centric: 1 / Highest resolution: 1.4 Å / Lowest resolution: 15 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 21483 / Reflection centric: 2923
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
6.77-151.630.40.2138104
4.38-6.771.510.40.2465170
3.23-4.381.180.30.2997250
2.56-3.231.450.20.11719326
2.12-2.561.60.20.12647404
1.81-2.122.050.10.13777484
1.58-1.813.730.105120555
1.4-1.585.850.106620630
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se14.41721-0.141-0.16-0.0490
2Se22.15480.002-0.067-0.0510
3Se25.59943-0.241-0.223-0.0190
4Se35.7292-0.248-0.2490.2750
5Se10.38099-0.212-0.2320.3040
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.77-150.3050.5350242138104
4.38-6.770.4230.5780635465170
3.23-4.380.4240.5301247997250
2.56-3.230.4560.543020451719326
2.12-2.560.450.518030512647404
1.81-2.120.3840.433042613777484
1.58-1.810.2820.312056755120555
1.4-1.580.1710.188072506620630
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 16497
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.24-100680.783506
4.16-5.2463.10.862508
3.61-4.1663.10.879507
3.27-3.6160.40.867506
3.03-3.27590.843505
2.85-3.0361.20.866508
2.7-2.8562.30.867513
2.58-2.757.70.875507
2.47-2.5861.50.851536
2.38-2.4763.70.868567
2.29-2.3857.80.885575
2.22-2.29610.879604
2.15-2.2255.20.891605
2.09-2.15590.89630
2.03-2.0954.90.876638
1.97-2.0360.60.887692
1.93-1.9758.60.867674
1.88-1.9355.90.845710
1.84-1.8860.10.86716
1.8-1.8462.40.834727
1.76-1.861.60.841742
1.72-1.76620.846749
1.69-1.7266.80.819797
1.66-1.6966.10.816785
1.63-1.6666.50.773801
1.6-1.6367.70.763889

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-3000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.4→40.76 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.04 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.082 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1246 5.1 %RANDOM
Rwork0.177 ---
all0.179 24407 --
obs0.179 24407 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.226 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 0 156 1247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211118
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9151526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96525.57752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66515173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.421154
X-RAY DIFFRACTIONr_chiral_restr0.0820.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02871
X-RAY DIFFRACTIONr_nbd_refined0.1930.2484
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2801
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.220
X-RAY DIFFRACTIONr_mcbond_it1.0581.5730
X-RAY DIFFRACTIONr_mcangle_it1.67221159
X-RAY DIFFRACTIONr_scbond_it2.8213439
X-RAY DIFFRACTIONr_scangle_it3.4644.5363
X-RAY DIFFRACTIONr_rigid_bond_restr2.1531169
X-RAY DIFFRACTIONr_sphericity_free4.0253156
X-RAY DIFFRACTIONr_sphericity_bonded2.61231091
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 92 -
Rwork0.207 1660 -
all-1752 -
obs--99.38 %

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