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- PDB-1qfv: HISTAMINE BINDING PROTEIN FROM FEMALE BROWN EAR RHIPICEPHALUS APP... -

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Basic information

Entry
Database: PDB / ID: 1qfv
TitleHISTAMINE BINDING PROTEIN FROM FEMALE BROWN EAR RHIPICEPHALUS APPENDICULATUS
ComponentsPROTEIN (FEMALE-SPECIFIC HISTAMINE BINDING PROTEIN 2)
KeywordsLIGAND BINDING PROTEIN / LIPOCALIN
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
HISTAMINE / Female-specific histamine-binding protein 2
Similarity search - Component
Biological speciesRhipicephalus appendiculatus (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.36 Å
AuthorsPaesen, G.C. / Adams, P.L. / Harlos, K. / Nuttal, P.A. / Stuart, D.I.
CitationJournal: Mol.Cell / Year: 1999
Title: Tick histamine-binding proteins: isolation, cloning, and three-dimensional structure.
Authors: Paesen, G.C. / Adams, P.L. / Harlos, K. / Nuttall, P.A. / Stuart, D.I.
History
DepositionApr 14, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (FEMALE-SPECIFIC HISTAMINE BINDING PROTEIN 2)
B: PROTEIN (FEMALE-SPECIFIC HISTAMINE BINDING PROTEIN 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8434
Polymers39,6212
Non-polymers2222
Water9,674537
1
A: PROTEIN (FEMALE-SPECIFIC HISTAMINE BINDING PROTEIN 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9222
Polymers19,8101
Non-polymers1111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (FEMALE-SPECIFIC HISTAMINE BINDING PROTEIN 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9222
Polymers19,8101
Non-polymers1111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.560, 74.400, 77.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (FEMALE-SPECIFIC HISTAMINE BINDING PROTEIN 2)


Mass: 19810.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus appendiculatus (arthropod)
Organ: SALIVARY GLAND / Plasmid: PACC129.1 / Genus (production host): Spodoptera / Cell line (production host): SPODOPTERA / Production host: Spodoptera (butterflies/moths) / Strain (production host): SF21 / References: UniProt: O77421
#2: Chemical ChemComp-HSM / HISTAMINE / Histamine


Mass: 111.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9N3 / Comment: neurotransmitter, hormone*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.1 MMES1reservoir
30.01 Mcobalt chloride hexahydrate1reservoir
41.8 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.072
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.36→20 Å / Num. obs: 108735 / % possible obs: 74.8 % / Redundancy: 2.7 % / Rsym value: 0.063
Reflection
*PLUS
Highest resolution: 1.36 Å / Lowest resolution: 20 Å / % possible obs: 74.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.183

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.36→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.182 --
obs-74586 74.8 %
Refinement stepCycle: LAST / Resolution: 1.36→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 16 537 3297
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.36 Å / Lowest resolution: 20 Å / Rfactor obs: 0.193 / Rfactor Rfree: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.6

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