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- PDB-1qr4: TWO FIBRONECTIN TYPE-III DOMAIN SEGMENT FROM CHICKEN TENASCIN -

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Basic information

Entry
Database: PDB / ID: 1qr4
TitleTWO FIBRONECTIN TYPE-III DOMAIN SEGMENT FROM CHICKEN TENASCIN
ComponentsPROTEIN (TENASCIN)
KeywordsSTRUCTURAL PROTEIN / TENASCIN / FIBRONECTIN TYPE-III / HEPARIN / EXTRACELLULAR MATRIX / ADHESION / FUSION PROTEIN
Function / homology
Function and homology information


collagen-containing extracellular matrix / cell adhesion / signaling receptor binding / extracellular space
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 domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / EGF-like domain, extracellular / EGF-like domain / Epidermal growth factor-like domain. ...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 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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPiontek, K. / Bisig, D.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Purification, crystallization and preliminary crystallographic studies of a two fibronectin type-III domain segment from chicken tenascin encompassing the heparin- and contactin-binding regions.
Authors: Bisig, D. / Weber, P. / Vaughan, L. / Winterhalter, K.H. / Piontek, K.
History
DepositionJun 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Dec 25, 2019Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.5Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (TENASCIN)
B: PROTEIN (TENASCIN)


Theoretical massNumber of molelcules
Total (without water)40,5222
Polymers40,5222
Non-polymers00
Water1,56787
1
A: PROTEIN (TENASCIN)


Theoretical massNumber of molelcules
Total (without water)20,2611
Polymers20,2611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (TENASCIN)


Theoretical massNumber of molelcules
Total (without water)20,2611
Polymers20,2611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.240, 57.940, 72.240
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.02028, -0.99977, 0.00645), (0.96191, 0.01775, -0.2728), (0.27262, 0.01173, 0.96205)8.77566, 32.93981, 5.69305
2given(0.80229, -0.59446, 0.05429), (0.59223, 0.78128, -0.19713), (0.07477, 0.19031, 0.97887)3.9971, 37.67947, 8.22607

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Components

#1: Protein PROTEIN (TENASCIN)


Mass: 20260.840 Da / Num. of mol.: 2 / Fragment: FNIII DOMAINS 5-6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cellular location: EXTRACELLULAR MATRIX / Plasmid: PDS9/56 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P10039
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 %
Description: DATA WERE COLLECTED AT THE SYNCHROTRON FACILITIES OF DESY/X31 AND ESRF/BM01A
Crystal growpH: 5
Details: 27% PEG2000, 100MM NAAC PH 4.5-5.0, 10-100 MM MGCL2/CACL2,
Crystal
*PLUS
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
227 %PEG20001drop
3100 mM1dropNaAc
450-100 mM1dropMgCl2

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. obs: 11344 / % possible obs: 94 % / Redundancy: 6 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 13
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2 / Rsym value: 0.47 / % possible all: 70.1
Reflection
*PLUS
Num. measured all: 68031
Reflection shell
*PLUS
% possible obs: 75.5 % / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
X-PLORmodel building
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FNF

1fnf


Resolution: 2.55→17.8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1171 10 %RANDOM
Rwork0.209 ---
obs0.209 11325 94 %-
Displacement parametersBiso mean: 49.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.36 Å
Luzzati d res low-12.5 Å
Luzzati sigma a0.48 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.55→17.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 0 87 2787
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.38
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.55→2.67 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.421 90
Rwork0.377 838
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 17.8 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.38
LS refinement shell
*PLUS
Rfactor Rfree: 0.421 / Rfactor Rwork: 0.377

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