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- PDB-1t3x: Three Crystal Structures of Human Coactosin-like Protein -

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Basic information

Entry
Database: PDB / ID: 1t3x
TitleThree Crystal Structures of Human Coactosin-like Protein
ComponentsCoactosin-like protein
KeywordsPROTEIN BINDING / BETA-SHEET
Function / homology
Function and homology information


site of polarized growth / regulation of actin filament polymerization / cortical actin cytoskeleton / defense response to fungus / actin filament binding / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / enzyme binding ...site of polarized growth / regulation of actin filament polymerization / cortical actin cytoskeleton / defense response to fungus / actin filament binding / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / enzyme binding / extracellular exosome / extracellular region / nucleus / cytosol
Similarity search - Function
Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Coactosin-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, L. / Wei, Z. / Chen, Z. / Wang, Y.
CitationJournal: TO BE PUBLISHED
Title: Three Crystal Structures of Human Coactosin-like Protein
Authors: Liu, L. / Wei, Z. / Chen, Z. / Wang, Y.
History
DepositionApr 28, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coactosin-like protein


Theoretical massNumber of molelcules
Total (without water)15,8351
Polymers15,8351
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.414, 48.694, 72.642
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 Coactosin-like protein


Mass: 15834.767 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET22B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14019
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.06 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: TRIS-HCL, NACL, IMIDAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→11.87 Å / Num. obs: 9391 / Rmerge(I) obs: 0.034
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.125

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→11.75 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 395283.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 974 10.4 %RANDOM
Rwork0.212 ---
all0.217 ---
obs0.212 9357 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.079 Å2 / ksol: 0.388229 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å20 Å20 Å2
2--1.08 Å20 Å2
3----3.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→11.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 0 139 1177
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 163 10.6 %
Rwork0.257 1375 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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