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- PDB-1jc9: TACHYLECTIN 5A FROM TACHYPLEUS TRIDENTATUS (JAPANESE HORSESHOE CRAB) -

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Basic information

Entry
Database: PDB / ID: 1jc9
TitleTACHYLECTIN 5A FROM TACHYPLEUS TRIDENTATUS (JAPANESE HORSESHOE CRAB)
Componentstechylectin-5A
KeywordsSUGAR BINDING PROTEIN / lectin / fibrinogen related
Function / homology
Function and homology information


cell-cell adhesion / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
: / Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain ...: / Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / 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. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesTachypleus tridentatus (Chinese horseshoe crab)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.01 Å
AuthorsKairies, N. / Beisel, H.-G. / Fuentes-Prior, P. / Tsuda, R. / Muta, T. / Iwanaga, S. / Bode, W. / Huber, R. / Kawabata, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: The 2.0-A crystal structure of tachylectin 5A provides evidence for the common origin of the innate immunity and the blood coagulation systems.
Authors: Kairies, N. / Beisel, H.G. / Fuentes-Prior, P. / Tsuda, R. / Muta, T. / Iwanaga, S. / Bode, W. / Huber, R. / Kawabata, S.
History
DepositionJun 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). UNDER PHYSIOLOGICAL CONDITIONS TL5A FORMS HEXAMERIC OR OCTAMERIC ARRANGEMENTS, BUT THE PACKING DOES NOT ALLOW CREATION OF HEXAMERIC OR OCTAMERIC OLIGOMERIZATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: techylectin-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4853
Polymers31,2231
Non-polymers2612
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.934, 108.934, 64.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein techylectin-5A


Mass: 31223.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tachypleus tridentatus (Chinese horseshoe crab)
References: UniProt: Q9U8W8
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 8000, HEPES, Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-7 mg/mlprotein1drop
20.1 MHEPES1reservoir
310 %PEG80001reservoir
48 %ethylene glycol1reservoirpH7.0

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 21, 2000 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→15.25 Å / Num. all: 49191 / Num. obs: 48257 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 25.24 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 4.3
Reflection shellResolution: 2.01→2.13 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.344 / % possible all: 94.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
CNS1refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.01→15.25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: 44 residues N-terminal and 5 residues C-terminal could not be resolved due to badly defined electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2412 -RANDOM
Rwork0.183 ---
all-48257 --
obs-48257 98.1 %-
Displacement parametersBiso mean: 27.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å6.29 Å
Refinement stepCycle: LAST / Resolution: 2.01→15.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 16 179 2034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.41
X-RAY DIFFRACTIONc_mcangle_it2.01
LS refinement shellResolution: 2.01→2.13 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.291 423 -
Rwork0.27 --
obs-8473 90.8 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.291 / Rfactor Rwork: 0.27

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