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- PDB-4hfo: Biogenic amine-binding protein selenomethionine derivative -

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Basic information

Entry
Database: PDB / ID: 4hfo
TitleBiogenic amine-binding protein selenomethionine derivative
ComponentsBiogenic amine-binding protein
Keywordsamine-binding protein / Beta barrel / Serotonin / norepinephrine / Salivary gland
Function / homology
Function and homology information


histamine binding / nitric oxide binding / extracellular region
Similarity search - Function
Nitrophorin domain / Nitrophorin / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biogenic amine-binding protein
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAndersen, J.F. / Xu, X. / Chang, B. / Mans, B.J. / Ribeiro, J.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure and ligand-binding properties of the biogenic amine-binding protein from the saliva of a blood-feeding insect vector of Trypanosoma cruzi.
Authors: Xu, X. / Chang, B.W. / Mans, B.J. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionOct 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biogenic amine-binding protein
B: Biogenic amine-binding protein
C: Biogenic amine-binding protein
D: Biogenic amine-binding protein
I: Biogenic amine-binding protein
J: Biogenic amine-binding protein
K: Biogenic amine-binding protein
L: Biogenic amine-binding protein


Theoretical massNumber of molelcules
Total (without water)177,3718
Polymers177,3718
Non-polymers00
Water0
1
A: Biogenic amine-binding protein


Theoretical massNumber of molelcules
Total (without water)22,1711
Polymers22,1711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Biogenic amine-binding protein


Theoretical massNumber of molelcules
Total (without water)22,1711
Polymers22,1711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Biogenic amine-binding protein


Theoretical massNumber of molelcules
Total (without water)22,1711
Polymers22,1711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Biogenic amine-binding protein


Theoretical massNumber of molelcules
Total (without water)22,1711
Polymers22,1711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
I: Biogenic amine-binding protein


Theoretical massNumber of molelcules
Total (without water)22,1711
Polymers22,1711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
J: Biogenic amine-binding protein


Theoretical massNumber of molelcules
Total (without water)22,1711
Polymers22,1711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
K: Biogenic amine-binding protein


Theoretical massNumber of molelcules
Total (without water)22,1711
Polymers22,1711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
L: Biogenic amine-binding protein


Theoretical massNumber of molelcules
Total (without water)22,1711
Polymers22,1711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.164, 70.661, 108.413
Angle α, β, γ (deg.)90.000, 99.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Biogenic amine-binding protein


Mass: 22171.396 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q86PT9

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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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2006
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 30762 / Num. obs: 30762 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.1 / Χ2: 1.445 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.118.10.38230501.15199.5
3.11-3.238.30.29630491.142199.5
3.23-3.388.40.22230341.164199.6
3.38-3.568.40.16630631.199199.7
3.56-3.788.40.12230721.242199.7
3.78-4.078.40.09830331.252199.7
4.07-4.488.30.07330801.359199.8
4.48-5.138.30.06931021.647199.9
5.13-6.468.10.07431061.6781100
6.46-507.90.05331732.638199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→42.662 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6675 / SU ML: 1.17 / σ(F): 1.91 / Phase error: 38.71 / Stereochemistry target values: ML_SAD
RfactorNum. reflection% reflectionSelection details
Rfree0.3487 2988 5.02 %RANDOM
Rwork0.3211 ---
obs0.3225 30762 99.39 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.344 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso max: 559.39 Å2 / Biso mean: 83.6175 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--7.2698 Å2-0 Å2-11.9263 Å2
2---4.114 Å20 Å2
3---1.8191 Å2
Refinement stepCycle: LAST / Resolution: 3→42.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12360 0 0 0 12360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512628
X-RAY DIFFRACTIONf_angle_d0.91217018
X-RAY DIFFRACTIONf_chiral_restr0.0721842
X-RAY DIFFRACTIONf_plane_restr0.0032188
X-RAY DIFFRACTIONf_dihedral_angle_d12.4324634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.04990.4981080.40752608271696
3.0499-3.10250.43661510.407626982849100
3.1025-3.15890.3921430.398326972840100
3.1589-3.21960.45231450.405327252870100
3.2196-3.28530.40111380.369526932831100
3.2853-3.35670.40181230.390527602883100
3.3567-3.43470.35921280.365326512779100
3.4347-3.52060.43181370.357727252862100
3.5206-3.61570.33831530.318526752828100
3.6157-3.72210.36631260.335427732899100
3.7221-3.84210.38681450.324626252770100
3.8421-3.97940.26551350.333327482883100
3.9794-4.13860.30941650.321627052870100
4.1386-4.32680.29831560.302926442800100
4.3268-4.55460.26791530.280427072860100
4.5546-4.83960.2981390.235127082847100
4.8396-5.21270.30771660.299426892855100
5.2127-5.73610.41991350.295627122847100
5.7361-6.56360.38961680.323426882856100
6.5636-8.25960.38111350.329627122847100
8.2596-42.66580.30991390.25482589272896
Refinement TLS params.Method: refined / Origin x: 21.156 Å / Origin y: 24.0066 Å / Origin z: 26.8577 Å
111213212223313233
T-0.2022 Å20.0854 Å2-0.1478 Å2--0.1112 Å20.0446 Å2---0.1909 Å2
L-0.0487 °2-0.0192 °20.0823 °2-0.1009 °2-0.079 °2--0.0398 °2
S0.225 Å °0.0424 Å °0.2887 Å °-0.1299 Å °-0.0364 Å °-0.0342 Å °0.0467 Å °0.1282 Å °0.1271 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 196
2X-RAY DIFFRACTION1ALLB2 - 195
3X-RAY DIFFRACTION1ALLC4 - 196
4X-RAY DIFFRACTION1ALLD2 - 195
5X-RAY DIFFRACTION1ALLI2 - 196
6X-RAY DIFFRACTION1ALLJ2 - 195
7X-RAY DIFFRACTION1ALLK4 - 196
8X-RAY DIFFRACTION1ALLL2 - 195

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