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- PDB-2rb8: High resolution design of a protein loop -

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Basic information

Entry
Database: PDB / ID: 2rb8
TitleHigh resolution design of a protein loop
ComponentsTenascin
KeywordsCELL ADHESION / Beta sheet / loop design / Alternative splicing / Coiled coil / EGF-like domain / Extracellular matrix / Glycoprotein / Phosphorylation / Polymorphism / Secreted
Function / homology
Function and homology information


perisynaptic extracellular matrix / tenascin complex / interstitial matrix / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / cellular response to prostaglandin D stimulus / syndecan binding / response to fibroblast growth factor / cellular response to vitamin D ...perisynaptic extracellular matrix / tenascin complex / interstitial matrix / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / cellular response to prostaglandin D stimulus / syndecan binding / response to fibroblast growth factor / cellular response to vitamin D / prostate gland epithelium morphogenesis / negative regulation of cell adhesion / extracellular matrix structural constituent / Syndecan interactions / neuromuscular junction development / odontogenesis of dentin-containing tooth / basement membrane / ECM proteoglycans / Integrin cell surface interactions / regulation of cell adhesion / response to mechanical stimulus / cellular response to retinoic acid / regulation of cell migration / morphogenesis of an epithelium / regulation of cell growth / Post-translational protein phosphorylation / response to wounding / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / integrin binding / regulation of inflammatory response / collagen-containing extracellular matrix / response to ethanol / cell adhesion / endoplasmic reticulum lumen / focal adhesion / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / membrane
Similarity search - Function
Tenascin, EGF-like domain / Tenascin EGF domain / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / EGF-like domain, extracellular / EGF-like domain ...Tenascin, EGF-like domain / Tenascin EGF domain / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / EGF-like domain, extracellular / EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHu, X. / Wang, H. / Ke, H. / Kuhlman, B.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: High-resolution design of a protein loop.
Authors: Hu, X. / Wang, H. / Ke, H. / Kuhlman, B.
History
DepositionSep 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tenascin


Theoretical massNumber of molelcules
Total (without water)11,6181
Polymers11,6181
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.781, 62.781, 53.793
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Tenascin / / TN / Tenascin-C / TN-C / Hexabrachion / Cytotactin / Neuronectin / GMEM / JI / Myotendinous antigen ...TN / Tenascin-C / TN-C / Hexabrachion / Cytotactin / Neuronectin / GMEM / JI / Myotendinous antigen / Glioma- associated-extracellular matrix antigen / GP 150-225


Mass: 11617.773 Da / Num. of mol.: 1 / Fragment: unp residues 802-896 / Mutation: M24F, P25K, S27L, Q28A, P29E, V30I, F33I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNC, HXB / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: P24821
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.8M sodium formate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 19928 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.5
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3 / Num. unique all: 744 / % possible all: 33.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ten

1ten


Resolution: 1.45→30 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The data in the structure factor file are twinned. Twinning operator= -h,-k,l; twinning fraction= 0.5
RfactorNum. reflectionSelection details
Rfree0.1958 1750 random
obs0.1702 19132 -
Displacement parametersBiso mean: 15.201 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms723 0 0 78 801
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.379

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