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- PDB-2j61: L-ficolin complexed to N-acetylglucosamine (forme C) -

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Basic information

Entry
Database: PDB / ID: 2j61
TitleL-ficolin complexed to N-acetylglucosamine (forme C)
Components(FICOLIN-2) x 2
KeywordsLECTIN / GLYCOPROTEIN / FICRINOGEN-LIKE / INNATE IMMUNITY / PATTERN RECOGNITION PROTEIN / COLLAGEN / IMMUNOLOGY / LECTIN- LIKE
Function / homology
Function and homology information


mannan binding / recognition of apoptotic cell / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / opsonization / complement activation, lectin pathway / carbohydrate derivative binding / collagen trimer ...mannan binding / recognition of apoptotic cell / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / opsonization / complement activation, lectin pathway / carbohydrate derivative binding / collagen trimer / serine-type endopeptidase complex / proteoglycan binding / Initial triggering of complement / antigen binding / calcium-dependent protein binding / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / blood microparticle / defense response to Gram-positive bacterium / external side of plasma membrane / signaling receptor binding / proteolysis / extracellular space / extracellular exosome / 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 / Fibrinogen, alpha/beta/gamma chain, 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. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGarlatti, V. / Gaboriaud, C.
CitationJournal: Embo J. / Year: 2007
Title: Structural Insights Into the Innate Immune Recognition Specificities of L- and H-Ficolins.
Authors: Garlatti, V. / Belloy, N. / Martin, L. / Lacroix, M. / Matsushita, M. / Endo, Y. / Fujita, T. / Fontecilla-Camps, J.C. / Arlaud, G.J. / Thielens, N.M. / Gaboriaud, C.
History
DepositionSep 21, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _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_asym_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_asym_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
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FICOLIN-2
B: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7885
Polymers49,4872
Non-polymers3013
Water1,11762
1
A: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0193
Polymers24,7571
Non-polymers2612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7692
Polymers24,7291
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.591, 79.591, 172.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-2013-

HOH

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Components

#1: Protein FICOLIN-2 / COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2 / FICOLIN-B / FICOLIN B / SERUM LECTIN P35 / EBP-37 ...COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2 / FICOLIN-B / FICOLIN B / SERUM LECTIN P35 / EBP-37 / HUCOLIN / L-FICOLIN


Mass: 24757.332 Da / Num. of mol.: 1 / Fragment: BINDING DOMAIN, RESIDUES 97-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLASMA / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q15485
#2: Protein FICOLIN-2 / COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2 / FICOLIN-B / FICOLIN B / SERUM LECTIN P35 / EBP-37 ...COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2 / FICOLIN-B / FICOLIN B / SERUM LECTIN P35 / EBP-37 / HUCOLIN / L-FICOLIN


Mass: 24729.318 Da / Num. of mol.: 1 / Fragment: BINDING DOMAIN, RESIDUES 97-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLASMA / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q15485
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDOMAINE C TERMINAL DIFFERENCE BETWEEN UNP SEQUENCE AND THE PROTEIN CRYSTALLIZED BECAUSE IT EXISTS ...DOMAINE C TERMINAL DIFFERENCE BETWEEN UNP SEQUENCE AND THE PROTEIN CRYSTALLIZED BECAUSE IT EXISTS POINTS OF POLYMORPHISME IN L FICOLIN. THE CDNA USED CORRESPONDS TO ONE REPANDED ALLELE AND THE SEQUENCE IN UNP TO AN OTHER

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 60.8 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9206
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9206 Å / Relative weight: 1
ReflectionResolution: 2.7→19.39 Å / Num. obs: 16911 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JC9

1jc9


Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.867 / SU B: 16.011 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R: 0.843 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 990 5.9 %RANDOM
Rwork0.207 ---
obs0.212 15836 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.49 Å2
Baniso -1Baniso -2Baniso -3
1-3.03 Å21.52 Å20 Å2
2--3.03 Å20 Å2
3----4.55 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 17 62 3537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213591
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.9144866
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2385430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1350.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022843
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2950.31995
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2740.5293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.337
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.55
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.34922122
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44433376
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.25231469
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.441490
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.79 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.396 98
Rwork0.241 1492

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