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- PDB-2pf5: Crystal Structure of the Human TSG-6 Link Module -

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Basic information

Entry
Database: PDB / ID: 2pf5
TitleCrystal Structure of the Human TSG-6 Link Module
ComponentsTumor necrosis factor-inducible protein TSG-6
KeywordsCELL ADHESION / LINK MODULE / HYALURONAN-BINDING DOMAIN / ALPHA/BETA DOMAIN
Function / homology
Function and homology information


fibronectin fibril organization / hyaluronan metabolic process / ovarian cumulus expansion / hyaluronic acid binding / negative regulation of neutrophil chemotaxis / carboxylesterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / negative regulation of osteoclast differentiation / fibronectin binding / negative regulation of BMP signaling pathway ...fibronectin fibril organization / hyaluronan metabolic process / ovarian cumulus expansion / hyaluronic acid binding / negative regulation of neutrophil chemotaxis / carboxylesterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / negative regulation of osteoclast differentiation / fibronectin binding / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / positive regulation of receptor clustering / negative regulation of inflammatory response / tertiary granule lumen / cell-cell signaling / ficolin-1-rich granule lumen / cell adhesion / positive regulation of cell migration / inflammatory response / calcium ion binding / Neutrophil degranulation / signal transduction / extracellular space / extracellular region
Similarity search - Function
: / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. ...: / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Tumor necrosis factor-inducible gene 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHigman, V.A. / Mahoney, D.J. / Noble, M.E.M. / Day, A.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Plasticity of the TSG-6 HA-binding loop and mobility in the TSG-6-HA complex revealed by NMR and X-ray crystallography
Authors: Higman, V.A. / Blundell, C.D. / Mahoney, D.J. / Redfield, C. / Noble, M.E. / Day, A.J.
History
DepositionApr 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor-inducible protein TSG-6
B: Tumor necrosis factor-inducible protein TSG-6
C: Tumor necrosis factor-inducible protein TSG-6
D: Tumor necrosis factor-inducible protein TSG-6
E: Tumor necrosis factor-inducible protein TSG-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,99712
Polymers54,7335
Non-polymers2,2657
Water7,458414
1
A: Tumor necrosis factor-inducible protein TSG-6


Theoretical massNumber of molelcules
Total (without water)10,9471
Polymers10,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tumor necrosis factor-inducible protein TSG-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8724
Polymers10,9471
Non-polymers9253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tumor necrosis factor-inducible protein TSG-6


Theoretical massNumber of molelcules
Total (without water)10,9471
Polymers10,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tumor necrosis factor-inducible protein TSG-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7763
Polymers10,9471
Non-polymers8292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Tumor necrosis factor-inducible protein TSG-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4573
Polymers10,9471
Non-polymers5112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.816, 75.870, 90.674
Angle α, β, γ (deg.)90.00, 103.42, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
12A
22B
32C
42D
52E

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: 4

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA1 - 621 - 62
21VALVALBB1 - 621 - 62
31VALVALCC1 - 621 - 62
41VALVALDD1 - 621 - 62
51ILEILEEE1 - 611 - 61
12PROPROAA74 - 9574 - 95
22PROPROBB74 - 9574 - 95
32PROPROCC74 - 9574 - 95
42PROPRODD74 - 9574 - 95
52PROPROEE74 - 9574 - 95

NCS ensembles :
ID
1
2

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Components

#1: Protein
Tumor necrosis factor-inducible protein TSG-6 / TNF- stimulated gene 6 protein / Hyaluronate-binding protein


Mass: 10946.578 Da / Num. of mol.: 5 / Fragment: LINK_MODULE, RESIDUES 36-133 IN PREPROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: See Day et al. (1996) Protein Expression & Purification 8, 1-16.
Gene: TNFAIP6, TSG6 / Plasmid: PRK172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P98066
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 4.12 Å3/Da / Density % sol: 70.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: A 2.5 ul drop formed from equal amounts of protein solution (7 mg/ml solution in approximately 25mM TrisHCl and 75mM NaCl) and well solution was equilibrated against 1 ml well solution (2 M ...Details: A 2.5 ul drop formed from equal amounts of protein solution (7 mg/ml solution in approximately 25mM TrisHCl and 75mM NaCl) and well solution was equilibrated against 1 ml well solution (2 M Ammonium Sulphate, 2 % v/v PEG 400 and 0.1M Sodium Hepes (pH 7.5)), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→88.04 Å / Num. obs: 69439 / % possible obs: 99.14 % / Redundancy: 4.08 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.35
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.98 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.51 / % possible all: 98.62

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Processing

Software
NameVersionClassification
DNAdata collection
DMmodel building
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UUH - crystal structure of CD44

1uuh


Resolution: 1.9→88.04 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.679 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22588 3499 5 %RANDOM
Rwork0.19439 ---
obs0.19596 65938 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.66 Å2
2--0.3 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→88.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 191 414 4348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214054
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9645412
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.8825487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.6720.909187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61515648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5851543
X-RAY DIFFRACTIONr_chiral_restr0.1180.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023016
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21909
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22604
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2329
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.2119
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8741.52365
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27323621
X-RAY DIFFRACTIONr_scbond_it2.08631978
X-RAY DIFFRACTIONr_scangle_it2.8744.51771
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A411medium positional0.30.5
12B411medium positional0.240.5
13C411medium positional0.430.5
14D411medium positional0.220.5
15E411medium positional0.40.5
21A164medium positional0.310.5
22B164medium positional0.290.5
23C164medium positional0.280.5
24D164medium positional0.210.5
25E164medium positional0.380.5
11A411medium thermal1.082
12B411medium thermal0.942
13C411medium thermal0.882
14D411medium thermal0.762
15E411medium thermal1.422
21A164medium thermal0.922
22B164medium thermal0.712
23C164medium thermal0.792
24D164medium thermal0.882
25E164medium thermal0.992
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 226 -
Rwork0.238 4835 -
obs--98.39 %

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