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- PDB-3gaq: Female-specific Histamine-Binding Protein, D24R Mutant -

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Basic information

Entry
Database: PDB / ID: 3gaq
TitleFemale-specific Histamine-Binding Protein, D24R Mutant
ComponentsFemale-specific histamine-binding protein 2
KeywordsIMMUNE SYSTEM / Lipocalin / Beta barrel
Function / homology
Function and homology information


amine binding / symbiont-mediated perturbation of host defenses / extracellular region
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
Female-specific histamine-binding protein 2
Similarity search - Component
Biological speciesRhipicephalus appendiculatus (arthropod)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsDennis, C.A. / Homans, S.W.
CitationJournal: To be Published
Title: Entropic contributions to binding in a 'Hydrophilic' Ligand-Protein Interaction
Authors: Syme, N.R. / Dennis, C.A. / Bronowska, A. / Paesen, G. / Homans, S.W.
History
DepositionFeb 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 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: Female-specific histamine-binding protein 2
B: Female-specific histamine-binding protein 2


Theoretical massNumber of molelcules
Total (without water)39,1942
Polymers39,1942
Non-polymers00
Water3,621201
1
A: Female-specific histamine-binding protein 2


Theoretical massNumber of molelcules
Total (without water)19,5971
Polymers19,5971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Female-specific histamine-binding protein 2


Theoretical massNumber of molelcules
Total (without water)19,5971
Polymers19,5971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.963, 56.610, 63.801
Angle α, β, γ (deg.)90.00, 107.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Female-specific histamine-binding protein 2 / FS-HBP2


Mass: 19597.230 Da / Num. of mol.: 2 / Mutation: D24R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus appendiculatus (arthropod)
Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O77421
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: Protein at 10 mg/ml mixed in a 1:1 ratio with reservoir containing: 2.6 M Ammonium Sulphate, 0.1 M Bicine, pH 8.2, and 10 % isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2008 / Details: mirrors
RadiationMonochromator: confocal max-flux optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→12 Å / Num. obs: 18800 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 34.75 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2735 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALAdata scaling
AMoREphasing
REFMAC5.5.0035refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1QFT

1qft


Resolution: 2.25→11.96 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.997 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.371 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 933 5 %RANDOM
Rwork0.229 ---
obs0.232 18787 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 71.03 Å2 / Biso mean: 46.094 Å2 / Biso min: 28.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20.81 Å2
2---0.52 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.25→11.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 0 201 2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222834
X-RAY DIFFRACTIONr_bond_other_d0.0010.021798
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9113862
X-RAY DIFFRACTIONr_angle_other_deg0.783.0044364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9935346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73625.952168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77815436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1371510
X-RAY DIFFRACTIONr_chiral_restr0.080.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023286
X-RAY DIFFRACTIONr_gen_planes_other00.02588
X-RAY DIFFRACTIONr_mcbond_it1.09421716
X-RAY DIFFRACTIONr_mcbond_other0.1892696
X-RAY DIFFRACTIONr_mcangle_it1.84332758
X-RAY DIFFRACTIONr_scbond_it0.89221118
X-RAY DIFFRACTIONr_scangle_it1.38331102
LS refinement shellResolution: 2.25→2.306 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 75 -
Rwork0.28 1258 -
all-1333 -
obs-1258 99.93 %

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