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- PDB-1qag: Actin binding region of the dystrophin homologue utrophin -

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Basic information

Entry
Database: PDB / ID: 1qag
TitleActin binding region of the dystrophin homologue utrophin
ComponentsUTROPHIN ACTIN BINDING REGION
KeywordsSTRUCTURAL PROTEIN / CALPONIN HOMOLOGY DOMAIN / DOMAIN SWAPPING / ACTIN BINDING / UTROPHIN / DYSTROPHIN
Function / homology
Function and homology information


synaptic signaling / dystrophin-associated glycoprotein complex / regulation of sodium ion transmembrane transporter activity / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / filopodium membrane / muscle organ development / positive regulation of cell-matrix adhesion / muscle contraction / filopodium ...synaptic signaling / dystrophin-associated glycoprotein complex / regulation of sodium ion transmembrane transporter activity / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / filopodium membrane / muscle organ development / positive regulation of cell-matrix adhesion / muscle contraction / filopodium / sarcolemma / neuromuscular junction / integrin binding / actin binding / postsynaptic membrane / cytoskeleton / protein kinase binding / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / membrane / plasma membrane / cytoplasm
Similarity search - Function
Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin ...Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Calponin homology (CH) domain / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsKeep, N.H. / Winder, S.J. / Moores, C.A. / Walke, S. / Norwood, F.L.M. / Kendrick-Jones, J.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of the actin-binding region of utrophin reveals a head-to-tail dimer
Authors: Keep, N.H. / Winder, S.J. / Moores, C.A. / Walke, S. / Norwood, F.L.M. / Kendrick-Jones, J.
History
DepositionMar 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UTROPHIN ACTIN BINDING REGION
B: UTROPHIN ACTIN BINDING REGION


Theoretical massNumber of molelcules
Total (without water)52,2252
Polymers52,2252
Non-polymers00
Water21612
1
A: UTROPHIN ACTIN BINDING REGION


Theoretical massNumber of molelcules
Total (without water)26,1121
Polymers26,1121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UTROPHIN ACTIN BINDING REGION


Theoretical massNumber of molelcules
Total (without water)26,1121
Polymers26,1121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-27 kcal/mol
Surface area21260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)150.145, 55.160, 80.420
Angle α, β, γ (deg.)90.00, 106.06, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe biological assembly is probably the monomer rather than the dimer. This may be in an open configuration as the chains are in the crystal or in a closed configuration with the regions A31-148 and B153-B256 in the crystal being formed by a single chain

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Components

#1: Protein UTROPHIN ACTIN BINDING REGION


Mass: 26112.334 Da / Num. of mol.: 2 / Fragment: RESIDUES 28-261 / Mutation: SELENOMETHIONINE REPLACES METHIONINE
Source method: isolated from a genetically manipulated source
Details: The biological assembly is probably the monomer rather than the dimer. This may be in an open configuration as the chains are in the crystal or in a closed configuration with the regions A31- ...Details: The biological assembly is probably the monomer rather than the dimer. This may be in an open configuration as the chains are in the crystal or in a closed configuration with the regions A31-148 and B153-B256 in the crystal being formed by a single chain
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P46939
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Sodium Acetate pH 4.7, 2.0 M unbuffered sodium formate., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Acetate11
2sodium formate11
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein1drop
22.0 M1reservoir
30.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9000, 0.9795, 0.9809
DetectorType: PRINCETON 2K / Detector: CCD / Date: Jan 21, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97951
30.98091
ReflectionHighest resolution: 3 Å / Num. all: 12342 / Num. obs: 12342 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 8
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1772 / % possible all: 97.2
Reflection
*PLUS
Lowest resolution: 24 Å
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
MLPHAREphasing
SHARPphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MAD / Resolution: 3→99 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Bulk solvent correction and ncs restraints (not strict) used in X-Plor. RESIDUES 31-146 and 156-254 IN CHAINS A AND B USED AS SEPARATE GROUPS WITH WEIGHT 50.0 FOR NCS RESTRAINT.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 607 5 %RANDOM
Rwork0.198 ---
all-12253 --
obs-12253 94.7 %-
Displacement parametersBiso mean: 44.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-99 Å
Luzzati sigma a0.46 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3642 0 0 12 3654
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.66
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 106 5.2 %
Rwork0.3 1918 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2EXTRAPARA.PROEXTRATOP.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.66
LS refinement shell
*PLUS
Rfactor Rfree: 0.354 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.3 / Rfactor obs: 0.3

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