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- PDB-1g5u: LATEX PROFILIN HEVB8 -

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Basic information

Entry
Database: PDB / ID: 1g5u
TitleLATEX PROFILIN HEVB8
ComponentsPROFILIN
KeywordsALLERGEN / ACTIN-BINDING PROTEIN
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 speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Ganglberger, E. / Breiteneder, H. / Almo, S.C.
Citation
Journal: To be Published
Title: A Comparative Structural Analysis of Allergen Profilins HEVB8 and BETV2
Authors: Fedorov, A.A. / Fedorov, E.V. / Ganglberger, E. / Breiteneder, H. / Almo, S.C.
#1: Journal: INT.ARCH.ALLERGY.IMMUNOL / Year: 2000
Title: Latex Allergy in Children
Authors: Niggemann, B. / Breiteneder, H.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: X-ray Structures of Isoforms of the Actin-binding Protein Profilin that Differ in their Affinity for Phosphatidylinositol Phosphates
Authors: Fedorov, A.A. / Magnus, K.A. / Graupe, M.H. / Lattman, E.E. / Pollard, T.D. / Almo, S.C.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: PURIFICATION, CHARACTERIZATION AND CRYSTALLIZATION OF HUMAN PLATELET PROFILIN EXPRESSED IN ESCHERICHIA COLI
Authors: FEDOROV, A.A. / POLLARD, T.D. / ALMO, S.C.
#4: Journal: 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. / M MAHONEY, N. / VALENTA, R. / ALMO, S.C.
#5: Journal: J.STRUCT.BIOL. / Year: 1998
Title: CRYSTAL PACKING INDUCES A COnFORMATIONAL CHANGE IN PROFILIN-I FROM ACANTHAMOEBA CASTELLANII
Authors: LIU, S. / FEDOROV, A.A. / POLLARD, T.D. / LATTMAN, E.E. / ALMO, S.C. / A MAGNUS, K.
#6: Journal: Nat.Struct.Biol. / Year: 1999
Title: PROFILIN BINDS PROLINE-RICH LIGANDS IN TWO DISTINCT AMIDE BACKBONE ORIENTATIONS
Authors: Mahoney, N.M. / Rozwarski, D.A. / Fedorov, E. / Fedorov, A.A. / Almo, S.C.
History
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: PROFILIN
B: PROFILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1213
Polymers28,0982
Non-polymers231
Water00
1
A: PROFILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0722
Polymers14,0491
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROFILIN


Theoretical massNumber of molelcules
Total (without water)14,0491
Polymers14,0491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.877, 58.877, 83.469
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsThe biological assembly is a monomer generated from the chain A or from the chain B

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Components

#1: Protein PROFILIN


Mass: 14048.929 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LEI8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium citrate, sucrose , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 22, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 7618 / Num. obs: 7618 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 18.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.8 / % possible all: 98.1

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A0K

1a0k


Resolution: 3.1→19.3 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 10000 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.313 598 10.6 %RANDOM
Rwork0.259 ---
all-5650 --
obs-5650 97 %-
Solvent computationSolvent model: flat model / Bsol: 43.85 Å2 / ksol: 0.242 e/Å3
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å23.55 Å20 Å2
2---2.54 Å20 Å2
3---5.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 1 0 1953
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it1.2571.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it1.4132
X-RAY DIFFRACTIONc_scangle_it2.3072.5
Refine LS restraints NCSNCS model details: restraints
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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