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- PDB-6zr0: Crystal structure of tetrameric fibrinogen-like recognition domai... -

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Basic information

Entry
Database: PDB / ID: 6zr0
TitleCrystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with N-acetylalanine 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-ACETYLALANINE / Fibrinogen C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsShrive, A.K. / Greenhough, T.J. / Williams, H.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Science and Technology Funding CouncilMX10369 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 1.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.2Jan 10, 2024Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)52,64614
Polymers51,3762
Non-polymers1,27012
Water4,468248
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)106,13932
Polymers102,7524
Non-polymers3,38728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,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)104,44624
Polymers102,7524
Non-polymers1,69420
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)119.219, 119.219, 44.180
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 / Sugars , 2 types, 3 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
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 259 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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C2H4O2
#7: Chemical ChemComp-AYA / N-ACETYLALANINE


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 59.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.5 M Ammonium Sulphate, 8% 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→84.44 Å / Num. obs: 46069 / % possible obs: 99.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.4
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.401 / Num. unique obs: 3105 / % possible all: 98.8

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Processing

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

4m7h


Resolution: 1.94→84.44 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.109 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2344 5.1 %RANDOM
Rwork0.189 ---
obs0.19 43722 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.83 Å2 / Biso mean: 21.69 Å2 / Biso min: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.35 Å2
Refinement stepCycle: final / Resolution: 1.94→84.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 77 248 3833
Biso mean--48.07 33.59 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133690
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183074
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.6575007
X-RAY DIFFRACTIONr_angle_other_deg1.1461.5997084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8535434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.91220.94234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74815520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1181532
X-RAY DIFFRACTIONr_chiral_restr0.0450.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02948
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 196 -
Rwork0.255 3195 -
all-3391 -
obs--98.83 %

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