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- PDB-6zqy: Crystal structure of tetrameric fibrinogen-like recognition domai... -

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Basic information

Entry
Database: PDB / ID: 6zqy
TitleCrystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with Neu5Ac ligand bound
ComponentsFibrinogen C domain-containing protein 1
KeywordsSUGAR BINDING PROTEIN / fibrinogen-like domain / N-acetyl-binding protein
Function / homology
Function and homology information


chitin binding / collagen-containing extracellular matrix / extracellular space / membrane / metal ion binding
Similarity search - Function
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.
Similarity search - Domain/homology
ACETIC ACID / N-acetyl-beta-neuraminic acid / Fibrinogen C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsShrive, A.K. / Greenhough, T.J. / Williams, H.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Science and Technology Funding CouncilMX310 United Kingdom
Citation
Journal: J.Biol.Chem. / Year: 2023
Title: Crystal structures of human immune protein FIBCD1 suggest an extended binding site compatible with recognition of pathogen associated carbohydrate motifs
Authors: Williams, H.M. / Moeller, J.B. / Burns, I. / Schlosser, A. / Sorensen, G.L. / Greenhough, T.J. / Holmskov, U. / Shrive, A.K.
#1: Journal: J Biol Chem / Year: 2014
Title: Crystal structure of the tetrameric fibrinogen-like recognition domain of fibrinogen C domain containing 1 (FIBCD1) protein
Authors: Shrive, A.K. / Moeller, J.B. / Burns, I. / Paterson, J.M. / Shaw, A.J. / Schlosser, A. / Sorensen, G.L. / Greenhough, T.J. / Holmskov, U.
History
DepositionJul 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 2.0Dec 13, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _struct_conn.ptnr2_auth_seq_id
Revision 2.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.2Jan 10, 2024Group: Database references / Category: pdbx_related_exp_data_set
Revision 2.3Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibrinogen C domain-containing protein 1
B: Fibrinogen C domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,80412
Polymers51,3762
Non-polymers1,42810
Water6,305350
1
A: Fibrinogen C domain-containing protein 1
hetero molecules

A: Fibrinogen C domain-containing protein 1
hetero molecules

A: Fibrinogen C domain-containing protein 1
hetero molecules

A: Fibrinogen C domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,05624
Polymers102,7524
Non-polymers4,30420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
2
B: Fibrinogen C domain-containing protein 1
hetero molecules

B: Fibrinogen C domain-containing protein 1
hetero molecules

B: Fibrinogen C domain-containing protein 1
hetero molecules

B: Fibrinogen C domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,16124
Polymers102,7524
Non-polymers1,40920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)119.290, 119.290, 44.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fibrinogen C domain-containing protein 1


Mass: 25688.055 Da / Num. of mol.: 2 / Fragment: fibrinogen-like recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FIBCD1, UNQ701/PRO1346 / Plasmid: pNT-Bac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8N539

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID / N-Acetylneuraminic acid


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 358 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C2H4O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M Ammonium Sulphate, 9% Dioxane, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.85→59.72 Å / Num. obs: 52803 / % possible obs: 98.6 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.046 / Rrim(I) all: 0.089 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.8930.388965532000.7950.2580.469398.7
9.06-59.643.90.02517564470.9990.0140.02827.389.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M7H

4m7h


Resolution: 1.85→59.72 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.481 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 2688 5.1 %RANDOM
Rwork0.175 ---
obs0.1761 50114 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.16 Å2 / Biso mean: 16.788 Å2 / Biso min: 9.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å2-0 Å2
2--0.5 Å20 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 1.85→59.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 88 350 3958
Biso mean--37.82 30.62 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133717
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183084
X-RAY DIFFRACTIONr_angle_refined_deg1.261.6595051
X-RAY DIFFRACTIONr_angle_other_deg1.2661.5987117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3015436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.04320.894235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88815522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3591532
X-RAY DIFFRACTIONr_chiral_restr0.0590.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024290
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02949
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rwork0.233 3687 -
Rfree-191 -
obs--98.43 %

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