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- PDB-2x45: Crystal Structure of Arg r 1 in complex with histamine -

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Basic information

Entry
Database: PDB / ID: 2x45
TitleCrystal Structure of Arg r 1 in complex with histamine
ComponentsALLERGEN ARG R 1
KeywordsALLERGEN
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 / Allergen Arg r 1
Similarity search - Component
Biological speciesARGAS REFLEXUS (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPaesen, G.C. / Siebold, C. / Syme, N. / Harlos, K. / Graham, S.C. / Hilger, C. / Homans, S.W. / Hentges, F. / Stuart, D.I.
CitationJournal: To be Published
Title: Crystal Structure of the Allergen Arg R 1, a Histamine-Binding Lipocalin from a Soft Tick
Authors: Paesen, G.C. / Siebold, C. / Syme, N. / Harlos, K. / Graham, S.C. / Hilger, C. / Homans, S.W. / Hentges, F. / Stuart, D.I.
History
DepositionJan 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALLERGEN ARG R 1
B: ALLERGEN ARG R 1
C: ALLERGEN ARG R 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,56412
Polymers46,5643
Non-polymers1,0009
Water16,358908
1
A: ALLERGEN ARG R 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8554
Polymers15,5211
Non-polymers3333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALLERGEN ARG R 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8554
Polymers15,5211
Non-polymers3333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ALLERGEN ARG R 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8554
Polymers15,5211
Non-polymers3333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.147, 61.817, 63.871
Angle α, β, γ (deg.)90.00, 105.14, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.5019, 0.8649, 0.009191), (0.8649, -0.5019, 0.000519), (0.005062, 0.007689, -1)15.97, -27.71, 0.5632
2given(-0.4994, -0.8663, -0.01367), (0.8664, -0.4993, -0.005043), (-0.002457, -0.01436, 0.9999)-15.86, -27.46, 0.195
3given(0.4987, -0.8667, -0.006138), (-0.8668, -0.4987, -0.001613), (-0.001663, 0.006125, -1)-15.77, -27.65, 0.07579

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Components

#1: Protein ALLERGEN ARG R 1


Mass: 15521.223 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARGAS REFLEXUS (arthropod) / Organ: SALIVARY GLAND / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI(DE3)PLYSS / References: UniProt: Q5GQ85
#2: Chemical
ChemComp-HSM / HISTAMINE


Mass: 111.145 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C5H9N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / 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: 2.19 Å3/Da / Density % sol: 43.89 % / Description: NONE
Crystal growpH: 8.5
Details: 30% POLYETHYLENE GLYCOL 4000, 0.1 M TRIS.HCL, PH 8.5, 0.2 M SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 79040 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.1
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X46

2x46


Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.134 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18348 3948 5 %RANDOM
Rwork0.13041 ---
obs0.13302 75281 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.109 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20.26 Å2
2---0.28 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 72 908 4223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223612
X-RAY DIFFRACTIONr_bond_other_d0.0010.022492
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9664914
X-RAY DIFFRACTIONr_angle_other_deg0.8683.016097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31525.748127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29215658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.073153
X-RAY DIFFRACTIONr_chiral_restr0.0970.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02663
X-RAY DIFFRACTIONr_nbd_refined0.210.2697
X-RAY DIFFRACTIONr_nbd_other0.1990.22459
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21709
X-RAY DIFFRACTIONr_nbtor_other0.0870.21835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2689
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2050.26
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.284
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7581.52908
X-RAY DIFFRACTIONr_mcbond_other0.6041.5962
X-RAY DIFFRACTIONr_mcangle_it2.22223652
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.19631680
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8674.51230
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.46337585
X-RAY DIFFRACTIONr_sphericity_free7.5123908
X-RAY DIFFRACTIONr_sphericity_bonded2.68435995
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 293 -
Rwork0.193 5522 -
obs--99.93 %

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