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- PDB-1hqz: Cofilin homology domain of a yeast actin-binding protein ABP1P -

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Basic information

Entry
Database: PDB / ID: 1hqz
TitleCofilin homology domain of a yeast actin-binding protein ABP1P
ComponentsACTIN-BINDING PROTEIN
KeywordsSTRUCTURAL PROTEIN / cofilin homology domain / actin binding / New York SGX Research Center for Structural Genomics / NYSGXRC / Structural Genomics / PSI / Protein Structure Initiative
Function / homology
Function and homology information


protein localization to actin cortical patch / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch assembly / site of polarized growth / actin cortical patch / regulation of actin filament polymerization / mating projection tip / barbed-end actin filament capping / cortical actin cytoskeleton / actin filament binding ...protein localization to actin cortical patch / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch assembly / site of polarized growth / actin cortical patch / regulation of actin filament polymerization / mating projection tip / barbed-end actin filament capping / cortical actin cytoskeleton / actin filament binding / cell cortex / cytoplasm
Similarity search - Function
Fungal actin-binding protein 1, second SH3 domain / 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 / SH3 domain / Src homology 3 domains ...Fungal actin-binding protein 1, second SH3 domain / 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 / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Actin-binding protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, PHASED TRANSLATION FUNCTION, MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStrokopytov, B.V. / Fedorov, A.A. / Mahoney, N. / Drubin, D.G. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Phased translation function revisited: structure solution of the cofilin-homology domain from yeast actin-binding protein 1 using six-dimensional searches.
Authors: Strokopytov, B.V. / Fedorov, A. / Mahoney, N.M. / Kessels, M. / Drubin, D.G. / Almo, S.C.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure determination of yeast cofilin
Authors: Fedorov, A.A. / Lappalainen, P. / Fedorov, E.V. / Drubin, D.G. / Almo, S.C.
#2: Journal: Nature / Year: 1990
Title: Homology of a yeast actin-binding protein to signal transduction proteins and myosin-1
Authors: Drubin, D.G. / Mulholland, J. / Zhu, Z. / Botstein, D.
#3: Journal: J.Cell Biol. / Year: 1993
Title: Cofilin is an essential component of the yeast cortical cytoskeleton
Authors: Moon, A.L. / Janmey, P.A. / Louie, K.A. / Drubin, D.G.
History
DepositionDec 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: ACTIN-BINDING PROTEIN
2: ACTIN-BINDING PROTEIN
3: ACTIN-BINDING PROTEIN
4: ACTIN-BINDING PROTEIN
5: ACTIN-BINDING PROTEIN
6: ACTIN-BINDING PROTEIN
7: ACTIN-BINDING PROTEIN
8: ACTIN-BINDING PROTEIN
9: ACTIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)140,7469
Polymers140,7469
Non-polymers00
Water9,296516
1
1: ACTIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,6381
Polymers15,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
2: ACTIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,6381
Polymers15,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
3: ACTIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,6381
Polymers15,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
4: ACTIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,6381
Polymers15,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
5: ACTIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,6381
Polymers15,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
6: ACTIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,6381
Polymers15,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
7: ACTIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,6381
Polymers15,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
8: ACTIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,6381
Polymers15,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
9: ACTIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,6381
Polymers15,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
9: ACTIN-BINDING PROTEIN

9: ACTIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,2772
Polymers31,2772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2010 Å2
ΔGint-9 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.48, 66.68, 125.10
Angle α, β, γ (deg.)90.0, 108.26, 90.0
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
119-9203-

HOH

DetailsThe biological assembly is a monomer

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Components

#1: Protein
ACTIN-BINDING PROTEIN / ABP1P


Mass: 15638.401 Da / Num. of mol.: 9 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P15891
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.22 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122-28 %PEG40001reservoir
20.3 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.04019 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04019 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 68718 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.397 / Num. unique all: 9605 / % possible all: 89.6
Reflection
*PLUS
Num. obs: 68796 / % possible obs: 96.6 % / Redundancy: 2.3 %
Reflection shell
*PLUS
% possible obs: 92.6 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMmodel building
X-PLORmodel building
CNSrefinement
DMphasing
X-PLORphasing
CNSphasing
RefinementMethod to determine structure: SIR, PHASED TRANSLATION FUNCTION, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COF

1cof


Resolution: 2.1→15 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 6875 10.1 %RANDOM
Rwork0.213 ---
obs0.215 67961 94.9 %-
Solvent computationSolvent model: FLAT / Bsol: 50.2239 Å2 / ksol: 0.3641 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9669 0 0 521 10190
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 1056 10 %
Rwork0.309 9407 -
obs-10463 87.8 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.358 / % reflection Rfree: 10 % / Rfactor Rwork: 0.309

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