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- PDB-6zr4: Crystal structure of tetrameric fibrinogen-like recognition domai... -

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Basic information

Entry
Database: PDB / ID: 6zr4
TitleCrystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1
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 beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile.
Similarity search - Domain/homology
ACETIC ACID / Fibrinogen C domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShrive, A.K. / Greenhough, T.J. / Williams, H.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Science and Technology Funding CouncilMX14692 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
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
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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)52,60312
Polymers51,3762
Non-polymers1,22710
Water4,216234
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)106,50828
Polymers102,7524
Non-polymers3,75524
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)103,90520
Polymers102,7524
Non-polymers1,15316
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)118.349, 118.349, 44.089
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: pcDNA3.1+ / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q8N539
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 243 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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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 Å3/Da / Density % sol: 59.07 % / Mosaicity: 0.29 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.7 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: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→83.83 Å / Num. obs: 41341 / % possible obs: 99.1 % / Redundancy: 3.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.067 / Rrim(I) all: 0.135 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1 / % possible all: 99.3

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2-2.053.60.3891090330000.8460.2250.4523.7
8.94-83.693.50.05917845140.9860.0350.06914.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.6.2data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4M7H

4m7h


Resolution: 2→83.83 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1351 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 2069 5 %RANDOM
Rwork0.1656 ---
obs0.1665 39268 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.6 Å2 / Biso mean: 16.274 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å2-0 Å2
2--0.55 Å20 Å2
3----1.1 Å2
Refinement stepCycle: final / Resolution: 2→83.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 74 234 3828
Biso mean--40.68 27.38 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133702
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183076
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.6575026
X-RAY DIFFRACTIONr_angle_other_deg1.2731.5987097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.315436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.62520.94234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14215522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0561532
X-RAY DIFFRACTIONr_chiral_restr0.0640.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02948
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 138 -
Rwork0.212 2860 -
all-2998 -
obs--99.27 %

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