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

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Basic information

Entry
Database: PDB / ID: 2rbl
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 / neuromuscular junction development / Syndecan interactions / 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 / response to ethanol / collagen-containing extracellular matrix / 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. / N-terminal domain of TfIIb - #10 / EGF-like domain, extracellular ...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. / N-terminal domain of TfIIb - #10 / EGF-like domain, extracellular / EGF-like domain / N-terminal domain of TfIIb / Epidermal growth factor-like domain. / Single Sheet / 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: 2.1 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 19, 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 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 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 1.4Aug 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

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Assembly

Deposited unit
A: Tenascin
B: Tenascin
M: Tenascin


Theoretical massNumber of molelcules
Total (without water)34,9463
Polymers34,9463
Non-polymers00
Water00
1
A: Tenascin
B: Tenascin


Theoretical massNumber of molelcules
Total (without water)23,2982
Polymers23,2982
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
MethodPISA
2
M: Tenascin


Theoretical massNumber of molelcules
Total (without water)11,6491
Polymers11,6491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.200, 137.200, 86.682
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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: 11648.830 Da / Num. of mol.: 3 / 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) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: P24821

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 2.0 M Ammonium Sulfate, pH = 3.0, 10% additive 0.1 M cupric chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 15770 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.1
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.1 / Num. unique all: 1106 / % possible all: 60.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SERGUIcontrol programdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1TEN

1ten


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.912 / SU B: 19.528 / SU ML: 0.23 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.31 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3 752 5 %RANDOM
Rwork0.25 ---
obs0.25 14973 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.204 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 0 0 2014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0420.0222039
X-RAY DIFFRACTIONr_angle_refined_deg3.331.9892774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9295253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.78326.45293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.25315363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.742159
X-RAY DIFFRACTIONr_chiral_restr0.2110.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021524
X-RAY DIFFRACTIONr_nbd_refined0.310.2854
X-RAY DIFFRACTIONr_nbtor_refined0.340.21315
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.22
X-RAY DIFFRACTIONr_mcbond_it1.9751.51355
X-RAY DIFFRACTIONr_mcangle_it2.85122108
X-RAY DIFFRACTIONr_scbond_it4.7673816
X-RAY DIFFRACTIONr_scangle_it6.6824.5666
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 32 -
Rwork0.285 752 -
obs--58.99 %

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