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- PDB-1pxy: Crystal structure of the actin-crosslinking core of Arabidopsis f... -

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Basic information

Entry
Database: PDB / ID: 1pxy
TitleCrystal structure of the actin-crosslinking core of Arabidopsis fimbrin
Componentsfimbrin-like protein
KeywordsSTRUCTURAL PROTEIN / CALPONIN HOMOLOGY / F-ACTIN-BINDING DOMAIN (ABD) / F-ACTIN-CROSSLINKING / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


actin filament network formation / actin filament bundle / actin filament bundle assembly / actin filament / circadian rhythm / actin filament binding / metal ion binding / cytoplasm
Similarity search - Function
Fimbrin/Plastin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. ...Fimbrin/Plastin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsKlein, M.G. / Shi, W. / Tseng, Y. / Wirtz, D. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Structure / Year: 2004
Title: Structure of the actin crosslinking core of fimbrin.
Authors: Klein, M.G. / Shi, W. / Ramagopal, U. / Tseng, Y. / Wirtz, D. / Kovar, D.R. / Staiger, C.J. / Almo, S.C.
History
DepositionJul 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fimbrin-like protein
B: fimbrin-like protein


Theoretical massNumber of molelcules
Total (without water)115,0952
Polymers115,0952
Non-polymers00
Water3,423190
1
A: fimbrin-like protein


Theoretical massNumber of molelcules
Total (without water)57,5481
Polymers57,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: fimbrin-like protein


Theoretical massNumber of molelcules
Total (without water)57,5481
Polymers57,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.688, 104.981, 104.411
Angle α, β, γ (deg.)90.00, 103.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein fimbrin-like protein


Mass: 57547.645 Da / Num. of mol.: 2 / Fragment: actin-crosslinking core, residues 123-623 / Mutation: V240L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pGEX4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7G188
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 6% PEG 8000, 100 mM Tris, 1mM DTT, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.984, 0.9786, 0.9789, 0.9560
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2001
RadiationMonochromator: Double flat crystal monochromator with fixed exit geometry
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9841
20.97861
30.97891
40.9561
ReflectionResolution: 2.4→30 Å / Num. all: 51046 / Num. obs: 44865 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.97 % / Rsym value: 0.067 / Net I/σ(I): 20.71
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.35 / Num. unique all: 4394 / Rsym value: 0.303 / % possible all: 86.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1AOA

1aoa


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 4559 -RANDOM
Rwork0.2293 ---
all0.2293 44865 --
obs0.2293 44865 93.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7518 0 0 190 7708
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection
Rfree0.3347 298
Rwork0.2761 -
obs-3167

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