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- PDB-1htn: HUMAN TETRANECTIN, A TRIMERIC PLASMINOGEN BINDING PROTEIN WITH AN... -

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Basic information

Entry
Database: PDB / ID: 1htn
TitleHUMAN TETRANECTIN, A TRIMERIC PLASMINOGEN BINDING PROTEIN WITH AN ALPHA-HELICAL COILED COIL
ComponentsTETRANECTINCLEC3B
KeywordsLECTIN / TETRANECTIN / PLASMINOGEN BINDING / KRINGLE 4 / ALPHA-HELICAL COILED COIL / C-TYPE LECTIN / CARBOHYDRATE RECOGNITION DOMAIN
Function / homology
Function and homology information


kringle domain binding / platelet dense granule lumen / granular component / positive regulation of plasminogen activation / cellular response to organic substance / bone mineralization / cellular response to transforming growth factor beta stimulus / ossification / Platelet degranulation / heparin binding ...kringle domain binding / platelet dense granule lumen / granular component / positive regulation of plasminogen activation / cellular response to organic substance / bone mineralization / cellular response to transforming growth factor beta stimulus / ossification / Platelet degranulation / heparin binding / carbohydrate binding / collagen-containing extracellular matrix / calcium ion binding / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNielsen, B.B. / Kastrup, J.S. / Rasmussen, H. / Holtet, T.L. / Graversen, J.H. / Etzerodt, M. / Thogersen, H.C. / Larsen, I.K.
Citation
Journal: FEBS Lett. / Year: 1997
Title: Crystal structure of tetranectin, a trimeric plasminogen-binding protein with an alpha-helical coiled coil.
Authors: Nielsen, B.B. / Kastrup, J.S. / Rasmussen, H. / Holtet, T.L. / Graversen, J.H. / Etzerodt, M. / Thogersen, H.C. / Larsen, I.K.
#1: Journal: Protein Sci. / Year: 1997
Title: Tetranectin, a Trimeric Plasminogen-Binding C-Type Lectin
Authors: Holtet, T.L. / Graversen, J.H. / Clemmensen, I. / Thogersen, H.C. / Etzerodt, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Human Plasminogen Binding Protein Tetranectin: Crystallization and Preliminary X-Ray Analysis of the C-Type Lectin Crd and the Full-Length Protein
Authors: Kastrup, J.S. / Rasmussen, H. / Nielsen, B.B. / Larsen, I.K. / Holtet, T.L. / Graversen, J.H. / Etzerodt, M. / Thogersen, H.C.
#3: Journal: FEBS Lett. / Year: 1992
Title: The Gene Structure of Tetranectin, a Plasminogen Binding Protein
Authors: Berglund, L. / Petersen, T.E.
History
DepositionMay 28, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TETRANECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3463
Polymers20,2661
Non-polymers802
Water64936
1
A: TETRANECTIN
hetero molecules

A: TETRANECTIN
hetero molecules

A: TETRANECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0389
Polymers60,7983
Non-polymers2406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)89.140, 89.140, 75.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein TETRANECTIN / CLEC3B


Mass: 20265.955 Da / Num. of mol.: 1 / Fragment: RESIDUES 26 - 181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PT7H6 / Production host: Escherichia coli (E. coli) / Strain (production host): DH / References: UniProt: P05452
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE NUMBERING OF RECOMBINANT TETRANECTIN (0 - 181) IN THIS ENTRY IS ACCORDING TO J. ...THE RESIDUE NUMBERING OF RECOMBINANT TETRANECTIN (0 - 181) IN THIS ENTRY IS ACCORDING TO J.FUHLENDORFF, I.CLEMMENSEN, S.MAGNUSSON. BIOCHEMISTRY 26, 6757-6764 (1987)).

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growMethod: reverse salting / pH: 8
Details: THE PROTEIN WAS CRYSTALLIZED BY THE REVERSE SALTING IN METHOD FROM A DROP CONTAINING 12.5-25 MM TRIS-HCL, PH 8.0, 25-50 MM NACL, 2MM CACL2, reverse salting
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.86 mg/mlprotein1drop
22.86 %isopropanol1drop
32.0 Mammonium sulfate1drop
42.14 %ethanol1drop
55 %ethanol1reservoir
62.1 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 5529 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 6.7
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.519 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4data reduction
AMoREphasing
X-PLOR3.851refinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MSB

2msb


Resolution: 2.8→6 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2.5
RfactorNum. reflection% reflectionSelection details
Rfree0.292 507 10.7 %RANDOM
Rwork0.223 ---
obs0.223 4748 95.5 %-
Displacement parametersBiso mean: 25.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 2 36 1250
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
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
LS refinement shellResolution: 2.8→2.96 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 74 10.3 %
Rwork0.298 643 -
obs--87.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29
LS refinement shell
*PLUS
Rfactor obs: 0.298

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