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- PDB-2x46: Crystal Structure of SeMet Arg r 1 -

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Basic information

Entry
Database: PDB / ID: 2x46
TitleCrystal Structure of SeMet Arg r 1
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
Biological speciesARGAS REFLEXUS (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1 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 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALLERGEN ARG R 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8142
Polymers15,6921
Non-polymers1221
Water5,260292
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.497, 55.661, 61.928
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 ALLERGEN ARG R 1


Mass: 15692.000 Da / Num. of mol.: 1 / Mutation: YES
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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 86 TO MSE
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: 1.78 Å3/Da / Density % sol: 31.08 % / 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: BM14 / Wavelength: 0.8
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2007
RadiationMonochromator: MAR CCD 225 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1→30 Å / Num. obs: 61187 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.8
Reflection shellResolution: 1→1.1 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 10 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.508 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15735 3053 5 %RANDOM
Rwork0.13535 ---
obs0.13639 58143 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.279 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 8 292 1385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221156
X-RAY DIFFRACTIONr_bond_other_d0.0160.02782
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9551576
X-RAY DIFFRACTIONr_angle_other_deg0.9923.0061931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77225.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.46415204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.583151
X-RAY DIFFRACTIONr_chiral_restr0.2750.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02212
X-RAY DIFFRACTIONr_nbd_refined0.210.2228
X-RAY DIFFRACTIONr_nbd_other0.1860.2827
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2582
X-RAY DIFFRACTIONr_nbtor_other0.090.2580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1460.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.265
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7731.5843
X-RAY DIFFRACTIONr_mcbond_other0.6631.5309
X-RAY DIFFRACTIONr_mcangle_it2.22221193
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0433500
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6284.5376
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.34832291
X-RAY DIFFRACTIONr_sphericity_free6.63292
X-RAY DIFFRACTIONr_sphericity_bonded3.75931906
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.143 230 -
Rwork0.138 4184 -
obs--98.55 %

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