+Open data
-Basic information
Entry | Database: PDB / ID: 1bhd | ||||||
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Title | SECOND CALPONIN HOMOLOGY DOMAIN FROM UTROPHIN | ||||||
Components | UTROPHIN | ||||||
Keywords | STRUCTURAL 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 / zinc ion binding / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Keep, N.H. / Winder, S.J. / Kendrick-Jones, J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bhd.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bhd.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 1bhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bhd_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 1bhd_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 1bhd_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 1bhd_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/1bhd ftp://data.pdbj.org/pub/pdb/validation_reports/bh/1bhd | HTTPS FTP |
-Related structure data
Related structure data | 1aa2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.601644, -0.050091, -0.797192), Vector: |
-Components
#1: Protein | 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: 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.24 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.6 / Details: pH 7.6 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 25, 1997 |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 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
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Displacement parameters | Biso mean: 31.23 Å2
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Refine analyze | Luzzati d res low obs: 20 Å / Luzzati sigma a obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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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 |