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- PDB-2yf2: Crystal structure of the oligomerisation domain of C4b-binding pr... -

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Basic information

Entry
Database: PDB / ID: 2yf2
TitleCrystal structure of the oligomerisation domain of C4b-binding protein from Gallus gallus
ComponentsC4B BINDING PROTEIN
KeywordsIMMUNE SYSTEM / COMPLEMENT SYSTEM
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #3730 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / ACETATE ION / :
Function and homology information
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.24 Å
AuthorsCaesar, J.J.E. / Hill, F. / Lea, S.M.
CitationJournal: To be Published
Title: Crystal Structure of the Oligomerisation Domain of C4B-Binding Protein from Gallus Gallus
Authors: Caesar, J.J.E. / Hill, F. / Lea, S.M.
History
DepositionApr 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C4B BINDING PROTEIN
B: C4B BINDING PROTEIN
C: C4B BINDING PROTEIN
D: C4B BINDING PROTEIN
E: C4B BINDING PROTEIN
F: C4B BINDING PROTEIN
G: C4B BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,96037
Polymers51,1317
Non-polymers1,82930
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21770 Å2
ΔGint-152.2 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.888, 140.238, 85.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2006-

HOH

21F-2005-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.2818, 0.852, -0.4413), (-0.9035, 0.0808, -0.4209), (-0.3229, 0.5173, 0.7925)-5.1714, 23.2285, 17.3146
2given(-0.1868, 0.0399, 0.9816), (-0.1183, 0.991, -0.0628), (-0.9752, -0.1279, -0.1804)-20.1804, 5.4375, 68.5931
3given(-0.879, -0.1244, 0.4603), (-0.1966, 0.9741, -0.1121), (-0.4344, -0.189, -0.8807)17.0793, 6.7504, 90.7551
4given(-0.9184, -0.0673, -0.3898), (-0.0174, 0.9914, -0.13), (0.3952, -0.1126, -0.9117)51.7655, 6.3281, 73.7097
5given(-0.1749, -0.0643, -0.9825), (-0.2398, 0.9706, -0.0208), (0.9549, 0.232, -0.1852)69.2343, -2.2242, 22.5974
6given(0.6066, -0.0618, -0.7926), (0.0257, 0.998, -0.0581), (0.7946, 0.0149, 0.6069)40.7083, 1.5481, 1.9279

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Components

#1: Protein
C4B BINDING PROTEIN


Mass: 7304.416 Da / Num. of mol.: 7 / Fragment: OLIGOMERISATION DOMAIN, RESIDUES 395-457 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PRSET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41(DE3) / References: UniProt: E1C2T5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 395 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 395 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 395 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 395 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 395 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 395 TO SER ENGINEERED RESIDUE IN CHAIN E, CYS 395 TO SER ENGINEERED RESIDUE IN CHAIN F, CYS 395 TO SER ENGINEERED RESIDUE IN CHAIN G, CYS 395 TO SER
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: 3.07 Å3/Da / Density % sol: 59.9 % / Description: NONE
Crystal growDetails: 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE, 8% PEG 3350, PH 4.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.24→85.46 Å / Num. obs: 23669 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 38.19 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.5
Reflection shellResolution: 2.24→2.36 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / % possible all: 79.6

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.24→55.06 Å / Cor.coef. Fo:Fc: 0.9068 / Cor.coef. Fo:Fc free: 0.8888 / SU R Cruickshank DPI: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.191 / SU Rfree Cruickshank DPI: 0.193
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1199 5.09 %RANDOM
Rwork0.2202 ---
obs0.2209 23563 95.63 %-
Displacement parametersBiso mean: 53.53 Å2
Baniso -1Baniso -2Baniso -3
1--23.3641 Å20 Å20 Å2
2--18.2062 Å20 Å2
3---5.1579 Å2
Refinement stepCycle: LAST / Resolution: 2.24→55.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2882 0 120 71 3073
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093010HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994013HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1088SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes96HARMONIC2
X-RAY DIFFRACTIONt_gen_planes395HARMONIC5
X-RAY DIFFRACTIONt_it3010HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.81
X-RAY DIFFRACTIONt_other_torsion16.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion387SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3639SEMIHARMONIC4
LS refinement shellResolution: 2.24→2.34 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2406 113 4.94 %
Rwork0.253 2174 -
all0.2523 2287 -
obs--95.63 %

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