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- PDB-1prq: ACANTHAMOEBA CASTELLANII PROFILIN IA -

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Basic information

Entry
Database: PDB / ID: 1prq
TitleACANTHAMOEBA CASTELLANII PROFILIN IA
ComponentsPROFILIN IA
KeywordsCONTRACTILE PROTEIN / ACTIN-BINDING PROTEIN
Function / homology
Function and homology information


actin monomer binding / actin cytoskeleton / actin cytoskeleton organization / 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 speciesAcanthamoeba castellanii (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFedorov, A.A. / Pollard, T.D. / Way, M. / Lattman, E.E. / Almo, S.C.
Citation
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. / Magnus, K.A.
#1: 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. / Mahoney, N.M. / Valenta, R. / Almo, S.C.
#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 Acanthamoeba Profilin Expressed in Escherichia Coli
Authors: Almo, S.C. / Pollard, T.D. / Way, M. / Lattman, E.E.
#4: Journal: Annu.Rev.Cell Biol. / Year: 1994
Title: Structure of Actin Binding Proteins: Insights About Function at Atomic Resolution
Authors: Pollard, T.D. / Almo, S. / Quirk, S. / Vinson, V. / Lattman, E.E.
History
DepositionAug 18, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROFILIN IA


Theoretical massNumber of molelcules
Total (without water)12,9621
Polymers12,9621
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.090, 37.400, 34.700
Angle α, β, γ (deg.)90.00, 109.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROFILIN IA


Mass: 12962.446 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba castellanii (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P68696
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.02 Å3/Da / Density % sol: 40 %
Crystal growpH: 8 / Details: 1.5 M SODIUM POTASSIUM TARTRATE, pH 8.0

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1991
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→43.1 Å / Num. obs: 3255 / % possible obs: 82.76 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.9

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REFINED ACANTHAMOEBA PROFILIN IB STRUCTURE (1ACF)

1acf


Resolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.141 --
obs-3117 82.1 %
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms972 0 0 56 1028
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.018
X-RAY DIFFRACTIONp_angle_d0.0280.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8521.5
X-RAY DIFFRACTIONp_mcangle_it1.4572
X-RAY DIFFRACTIONp_scbond_it1.682
X-RAY DIFFRACTIONp_scangle_it2.7733
X-RAY DIFFRACTIONp_plane_restr0.0080.02
X-RAY DIFFRACTIONp_chiral_restr0.1240.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.1930.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1630.3
X-RAY DIFFRACTIONp_planar_tor1.32
X-RAY DIFFRACTIONp_staggered_tor16.710
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.310
X-RAY DIFFRACTIONp_special_tor

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