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- PDB-3brn: Crystal Structure of AM182 Serotonin Complex -

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Basic information

Entry
Database: PDB / ID: 3brn
TitleCrystal Structure of AM182 Serotonin 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
SEROTONIN / Lipocalin
Similarity search - Component
Biological speciesArgas monolakensis (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipocalin
B: Lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0104
Polymers33,6572
Non-polymers3522
Water1,42379
1
A: Lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0052
Polymers16,8291
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0052
Polymers16,8291
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.694, 91.694, 37.836
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Lipocalin /


Mass: 16828.646 Da / Num. of mol.: 2
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: Q09JR9
#2: Chemical ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL / Serotonin


Mass: 176.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O / Comment: neurotransmitter*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 2000 MME, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→79.31 Å / Num. obs: 30083 / % possible obs: 99.4 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.097 / Χ2: 1.095 / Net I/σ(I): 16.6
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2952 / Χ2: 1.76 / % possible all: 97

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.51 Å
Translation2.5 Å23.51 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
MX-baseddata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→79.31 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.061 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1206 5 %RANDOM
Rwork0.222 ---
obs0.224 23961 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.938 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å2-0.67 Å20 Å2
2---1.34 Å20 Å2
3---2 Å2
Refinement stepCycle: LAST / Resolution: 2→79.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 26 79 2390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222385
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.963254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5955299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47524.706102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02715347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.722158
X-RAY DIFFRACTIONr_chiral_restr0.3730.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021860
X-RAY DIFFRACTIONr_nbd_refined0.2550.2994
X-RAY DIFFRACTIONr_nbtor_refined0.3230.21629
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3260.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.27
X-RAY DIFFRACTIONr_mcbond_it3.3781.51519
X-RAY DIFFRACTIONr_mcangle_it4.69122407
X-RAY DIFFRACTIONr_scbond_it6.91131009
X-RAY DIFFRACTIONr_scangle_it8.7494.5847
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 81 -
Rwork0.286 1680 -
all-1761 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 0.0904 Å / Origin y: 26.5729 Å / Origin z: -4.6386 Å
111213212223313233
T-0.003 Å2-0.018 Å20.1649 Å2--0.194 Å2-0.0114 Å2---0.0329 Å2
L0.7861 °2-1.0606 °21.0214 °2-2.6487 °2-0.2327 °2--2.454 °2
S-0.0513 Å °0.0671 Å °-0.1012 Å °-0.0319 Å °0.0651 Å °-0.1038 Å °0.5548 Å °0.0272 Å °-0.0138 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1576 - 157
2X-RAY DIFFRACTION1BB6 - 1576 - 157

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