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- PDB-5r5x: PanDDA analysis group deposition -- Crystal Structure of FIBRINOG... -

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Basic information

Entry
Database: PDB / ID: 5r5x
TitlePanDDA analysis group deposition -- Crystal Structure of FIBRINOGEN-LIKE GLOBE DOMAIN OF HUMAN TENASCIN-C in complex with Z1259335913
ComponentsTenascin C (Hexabrachion), isoform CRA_a
KeywordsIMMUNE SYSTEM / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / FIBRINOGEN-RELATED PROTEIN (FREP) / PRO-INFLAMMATORY / DAMAGE-ASSOCIATED MOLECULAR PATTERN (DAMP)
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 / syndecan binding / cellular response to prostaglandin D stimulus / 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 / syndecan binding / cellular response to prostaglandin D stimulus / 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 beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / EGF-like domain, extracellular ...Tenascin, EGF-like domain / Tenascin EGF domain / : / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-RWV / Tenascin C (Hexabrachion), isoform CRA_a / Tenascin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.56 Å
AuthorsCoker, J.A. / Bezerra, G.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Yue, W.W. / Marsden, B.D.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Coker, J.A. / Bezerra, G.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Yue, W.W. / Marsden, B.D.
History
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tenascin C (Hexabrachion), isoform CRA_a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4092
Polymers25,1841
Non-polymers2251
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 77.160, 71.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Tenascin C (Hexabrachion), isoform CRA_a


Mass: 25183.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNC, hCG_29852 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024R884, UniProt: P24821*PLUS
#2: Chemical ChemComp-RWV / 1-{1-[(2-methyl-1,3-thiazol-4-yl)methyl]piperidin-4-yl}methanamine


Mass: 225.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.96 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MORPHEUS 0.09M NPS, 0.1M BUFFER SYSTEM 3 PH = 8.5, 50% V/V PRECIPITANT MIX 1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.56→54.56 Å / Num. obs: 31407 / % possible obs: 99.7 % / Redundancy: 12 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.021 / Rrim(I) all: 0.075 / Net I/σ(I): 18.7 / Num. measured all: 376004 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.56-1.68.91.7432024522740.5960.6171.8521.399.5
6.98-54.5610.40.019451443310.0060.0273.5100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6QNV

6qnv


Resolution: 1.56→54.56 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.077 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1452 4.6 %RANDOM
Rwork0.1746 ---
obs0.1762 29899 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.77 Å2 / Biso mean: 25.665 Å2 / Biso min: 17.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å2-0 Å2-0 Å2
2--1.2 Å2-0 Å2
3----2.41 Å2
Refinement stepCycle: final / Resolution: 1.56→54.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 15 172 1864
Biso mean--42.89 41.19 -
Num. residues----211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131786
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171505
X-RAY DIFFRACTIONr_angle_refined_deg1.781.652415
X-RAY DIFFRACTIONr_angle_other_deg1.5641.6013481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3015218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.05922.315108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16715266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8531511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022109
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02440
X-RAY DIFFRACTIONr_mcbond_it2.2542.583866
X-RAY DIFFRACTIONr_mcbond_other2.2532.585867
X-RAY DIFFRACTIONr_mcangle_it3.3253.8791087
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 112 -
Rwork0.326 2154 -
all-2266 -
obs--99.34 %

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