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- PDB-1bhd: SECOND CALPONIN HOMOLOGY DOMAIN FROM UTROPHIN -

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Basic information

Entry
Database: PDB / ID: 1bhd
TitleSECOND CALPONIN HOMOLOGY DOMAIN FROM UTROPHIN
ComponentsUTROPHIN
KeywordsSTRUCTURAL PROTEIN / CALPONIN HOMOLOGY / ACTIN BINDING
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 / filopodium / muscle contraction ...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 / filopodium / muscle contraction / neuromuscular junction / sarcolemma / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKeep, N.H. / Winder, S.J. / Kendrick-Jones, J.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: The 2.0 A structure of the second calponin homology domain from the actin-binding region of the dystrophin homologue utrophin.
Authors: Keep, N.H. / Norwood, F.L. / Moores, C.A. / Winder, S.J. / Kendrick-Jones, J.
History
DepositionJun 5, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _exptl_crystal.density_percent_sol
Revision 1.4Aug 2, 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

Downloads & links

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Assembly

Deposited unit
A: UTROPHIN
B: UTROPHIN


Theoretical massNumber of molelcules
Total (without water)27,3572
Polymers27,3572
Non-polymers00
Water3,117173
1
A: UTROPHIN


Theoretical massNumber of molelcules
Total (without water)13,6791
Polymers13,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UTROPHIN


Theoretical massNumber of molelcules
Total (without water)13,6791
Polymers13,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.920, 32.210, 65.360
Angle α, β, γ (deg.)90.00, 116.25, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.601644, -0.050091, -0.797192), (0.040246, -0.998665, 0.032377), (-0.797749, -0.012604, 0.602857)
Vector: 38.351, 29.182, 56.11)

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Components

#1: Protein UTROPHIN /


Mass: 13678.681 Da / Num. of mol.: 2
Fragment: 2ND CALPONIN HOMOLOGY DOMAIN FROM ACTIN BINDING REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: MUSCLESkeletal muscle / Description: EXPRESSED IN ESCHERICHIA COLI / Cell line: BL21 / Cellular location: LINKS CYTOSKELETON TO PLASMA MEMBRANE / Gene: UTRN, DMDL / Organ: PLASMA / Plasmid: PSJW1 (T7) / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): UTRN DMDL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P46939
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.2 Å3/Da / Density % sol: 44.24 %
Crystal growpH: 7.6 / Details: pH 7.6
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
218 %PEG80001reservoir
30.1 Msodium acetate1reservoir
40.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 25, 1997
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→22 Å / Num. obs: 14514 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 23.85 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 10.8
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 5.9 / % possible all: 98.9
Reflection
*PLUS
Num. obs: 16459 / Num. measured all: 46728
Reflection shell
*PLUS
% possible obs: 98.9 % / Num. unique obs: 2296 / Num. measured obs: 6400

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1AA2

1aa2


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: 0.011 AROMATIC PLANAR DEVIATION VALUE ABOVE IS FOR PEPTIDE. ESTIMATED COORDINATE ERROR. ESD FROM SIGMAA (A) : 0.185 LOW RESOLUTION CUTOFF (A) : 20.0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 776 5 %RANDOM
Rwork0.185 ---
obs0.202 15622 99.5 %-
Displacement parametersBiso mean: 31.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.043 Å2-5.93 Å20 Å2
2--0 Å25.554 Å2
3----3.65 Å2
Refine analyzeLuzzati d res low obs: 20 Å / Luzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 0 173 1944
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.1673
X-RAY DIFFRACTIONp_mcangle_it4.2325
X-RAY DIFFRACTIONp_scbond_it6.196
X-RAY DIFFRACTIONp_scangle_it8.0510
X-RAY DIFFRACTIONp_plane_restr0.0231
X-RAY DIFFRACTIONp_chiral_restr0.1380.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.37
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.13 Å / Rfactor Rfree: 0.319 / Num. reflection Rfree: 132 / % reflection Rfree: 5 % / Rfactor obs: 0.188

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