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- PDB-1cqa: BIRCH POLLEN PROFILIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1cqa
TitleBIRCH POLLEN PROFILIN
ComponentsPROFILIN
KeywordsCONTRACTILE PROTEIN / ACTIN-BINDING PROTEIN / ALLERGEN
Function / homology
Function and homology information


actin binding / cytoskeleton / cytoplasm
Similarity search - Function
Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBetula pendula (European white birch)
MethodX-RAY DIFFRACTION / SINGLE ISOMORPHOUS REPLACEMENT, MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFedorov, A.A. / Ball, T. / Mahoney, N.M. / Valenta, R. / Almo, S.C.
CitationJournal: Structure / Year: 1997
Title: The molecular basis for allergen cross-reactivity: crystal structure and IgE-epitope mapping of birch pollen profilin.
Authors: Fedorov, A.A. / Ball, T. / Mahoney, N.M. / Valenta, R. / Almo, S.C.
History
DepositionJul 26, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROFILIN


Theoretical massNumber of molelcules
Total (without water)14,2931
Polymers14,2931
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.900, 59.900, 85.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PROFILIN /


Mass: 14293.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betula pendula (European white birch) / Cell: POLLEN / Production host: Escherichia coli (E. coli) / References: UniProt: P25816
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mammonium sulfate11
2100 mMMES11

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30.1 Å / Num. obs: 5973 / % possible obs: 91.6 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.1
Reflection
*PLUS
Rmerge(I) obs: 0.084

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Processing

Software
NameClassification
PHASESphasing
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: SINGLE ISOMORPHOUS REPLACEMENT, MOLECULAR REPLACEMENT
Resolution: 2.4→8 Å / σ(F): 2
Details: THE STRUCTURE WAS SOLVED BY COMBINATION OF THE SINGLE ISOMORPHOUS REPLACEMENT AND MOLECULAR REPLACEMENT METHODS.
RfactorNum. reflection% reflection
Rwork0.178 --
obs-5356 85.1 %
Displacement parametersBiso mean: 19.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 0 48 1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.018
X-RAY DIFFRACTIONp_angle_d0.0250.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0290.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8861.5
X-RAY DIFFRACTIONp_mcangle_it1.5682
X-RAY DIFFRACTIONp_scbond_it1.7562
X-RAY DIFFRACTIONp_scangle_it2.9193
X-RAY DIFFRACTIONp_plane_restr0.0080.02
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd0.1940.3
X-RAY DIFFRACTIONp_multtor_nbd0.1960.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.160.3
X-RAY DIFFRACTIONp_planar_tor1.22
X-RAY DIFFRACTIONp_staggered_tor18.210
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.110
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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