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- PDB-2j1g: L-ficolin complexed to N-acetyl-cystein -

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Basic information

Entry
Database: PDB / ID: 2j1g
TitleL-ficolin complexed to N-acetyl-cystein
ComponentsFICOLIN-2
KeywordsSUGAR BINDING PROTEIN / GLYCOPROTEIN / FICRINOGEN-LIKE / INNATE IMMUNITY / PATTERN RECOGNITION PROTEIN / LECTIN / 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
ACETATE ION / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / N-ACETYL-L-CYSTEINE / Ficolin-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionAug 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Mar 13, 2013Group: Other
Revision 1.4Apr 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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

Downloads & links

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Assembly

Deposited unit
A: FICOLIN-2
B: FICOLIN-2
C: FICOLIN-2
D: FICOLIN-2
E: FICOLIN-2
F: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,65123
Polymers148,3766
Non-polymers3,27517
Water15,025834
1
A: FICOLIN-2
B: FICOLIN-2
C: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,98911
Polymers74,1883
Non-polymers1,8018
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: FICOLIN-2
E: FICOLIN-2
F: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,66312
Polymers74,1883
Non-polymers1,4759
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.040, 99.040, 142.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 24729.318 Da / Num. of mol.: 6 / 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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 849 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O8
#7: Chemical ChemComp-SC2 / N-ACETYL-L-CYSTEINE / (2R)-2-acetamido-3-sulfanyl-propanoic acid


Type: peptide-like / Mass: 163.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO3S / Comment: medication*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 834 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsC-TERMINAL DOMAIN CONFLICTS BETWEEN UNP SEQUENCE AND COORDINATES: THERE IS A DIFFERENCE BECAUSE ...C-TERMINAL DOMAIN CONFLICTS BETWEEN UNP SEQUENCE AND COORDINATES: THERE IS A DIFFERENCE BECAUSE POINTS OF POLYMORPHISM EXIST IN L FICOLIN FOR 247 AND 168. THE CDNA USED CORRESPONDS TO ONE WIDESPREAD ALLELE AND THE SEQUENCE IN UNP TO ANOTHER

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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: 2.54 Å3/Da / Density % sol: 51.27 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97564
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97564 Å / Relative weight: 1
ReflectionResolution: 1.95→19.6 Å / Num. obs: 111804 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDP ENTRY 2J3G

2j3g


Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.476 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 5661 5 %RANDOM
Rwork0.176 ---
obs0.178 107549 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10249 0 167 834 11250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02110729
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.92514524
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85551278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.26423.595573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.451151633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7731573
X-RAY DIFFRACTIONr_chiral_restr0.0910.21458
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028458
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.34877
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.57099
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.51488
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.365
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.559
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8826461
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.324310046
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.41834987
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.06544478
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: 1.95→2.02 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.257 548
Rwork0.213 10401
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.19144.1384-1.09868.6689-1.59012.53690.2961-0.50730.4345-0.4055-0.41620.67810.31870.10430.1201-0.06350.1483-0.042-0.1641-0.0917-0.13873.07946.0684.432
20.7517-0.17270.21481.58370.22941.6680.0760.0184-0.18780.0139-0.02780.03980.5511-0.0391-0.04820.090.0146-0.0264-0.0861-0.0242-0.0291-7.0150.3965.067
30.58120.02850.17081.98641.09971.79630.0126-0.07140.02330.53850.1202-0.31960.3390.1486-0.13290.10570.011-0.0292-0.0811-0.030.0263-5.91540.0331.211
41.9678-0.25380.22224.76450.64982.0930.13220.26750.1018-0.6856-0.0788-0.40330.07910.389-0.0534-0.13740.08560.04260.0606-0.0345-0.104837.91781.01716.323
52.2926-0.02430.24240.56030.14291.2852-0.0456-0.0187-0.28770.06190.02690.11820.1466-0.38740.0187-0.10270.04710.03060.06370.0085-0.042247.01275.00416.017
63.85980.5377-4.44371.3913-0.3628.10460.45241.19740.2548-0.2133-0.05160.1285-1.0795-1.6427-0.40080.00250.23630.06120.24460.0332-0.066837.60770.21119.89
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A76 - 287
2X-RAY DIFFRACTION2B75 - 288
3X-RAY DIFFRACTION3C75 - 288
4X-RAY DIFFRACTION4D75 - 288
5X-RAY DIFFRACTION5E75 - 288
6X-RAY DIFFRACTION6F75 - 288

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