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- PDB-1ok3: Decay accelerating factor (cd55): the structure of an intact huma... -

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Basic information

Entry
Database: PDB / ID: 1ok3
TitleDecay accelerating factor (cd55): the structure of an intact human complement regulator.
ComponentsCOMPLEMENT DECAY-ACCELERATING FACTOR
KeywordsREGULATOR OF COMPLEMENT PATHWAY / REGULATOR OF COMPLEMENT / DECAY ACCELERATION OF C3/C5 CONVERTASES / PATHOGEN RECEPTOR / SHORT CONSENSUS REPEAT DOMAINS
Function / homology
Function and homology information


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / COPI-mediated anterograde transport ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / COPI-mediated anterograde transport / complement activation, classical pathway / side of membrane / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / Regulation of Complement cascade / positive regulation of T cell cytokine production / virus receptor activity / positive regulation of cytosolic calcium ion concentration / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / cell surface / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Complement decay-accelerating factor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Crispin, M.D.M. ...Lukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Crispin, M.D.M. / Radcliffe, C.M. / Dwek, R.A. / Evans, D.J. / Morgan, B.P. / Smith, R.A.G. / Lea, S.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Complement Regulation at the Molecular Level: The Structure of Decay-Accelerating Factor
Authors: Lukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Harvey, D.J. / Crispin, M.D.M. / Radcliffe, C.M. / Dwek, R.A. ...Authors: Lukacik, P. / Roversi, P. / White, J. / Esser, D. / Smith, G.P. / Billington, J. / Williams, P.A. / Rudd, P.M. / Wormald, M.R. / Harvey, D.J. / Crispin, M.D.M. / Radcliffe, C.M. / Dwek, R.A. / Evans, D.J. / Morgan, B.P. / Smith, R.A.G. / Lea, S.M.
#1: Journal: Protein Sci. / Year: 2004
Title: Biological Activity, Membrane-Targeting Modification, and Crystallization of Soluble Human Decay Accelerating Factor Expressed in E. Coli
Authors: White, J. / Lukacik, P. / Esser, D. / Steward, M. / Giddings, N. / Bright, J.R. / Fritchley, S. / Morgan, B.P. / Lea, S.M. / Smith, G.P. / Smith, R.A.G.
History
DepositionJul 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 7, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: COMPLEMENT DECAY-ACCELERATING FACTOR
B: COMPLEMENT DECAY-ACCELERATING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,79417
Polymers56,5372
Non-polymers1,25715
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.670, 55.080, 61.650
Angle α, β, γ (deg.)86.47, 84.37, 64.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein COMPLEMENT DECAY-ACCELERATING FACTOR / CD55 / CR / DAF


Mass: 28268.455 Da / Num. of mol.: 2 / Fragment: FOUR EXTRACELLULAR SCR DOMAINS, RESIDUES 35-285
Source method: isolated from a genetically manipulated source
Details: MODELLED GLYCEROLS, ACETATES AND SULPHATES FROM CRYSTALLISATION BUFFER
Source: (gene. exp.) HOMO SAPIENS (human)
Description: HUMAN SEQUENCE EXPRESSED IN E.COLI.. SEMET SUBSTITUTION
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BA34 / References: UniProt: P08174
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES A48 AND B48 MAP ONTO RESIDUE 80 OF SWISSPROT ENTRY P08174. RESIDUE 80 IN THE SWISSPROT ...RESIDUES A48 AND B48 MAP ONTO RESIDUE 80 OF SWISSPROT ENTRY P08174. RESIDUE 80 IN THE SWISSPROT ENTRY IS GIVEN AS THR, BUT SOME REFERENCES FOR SWS P08174 SHOW RESIDUE 80 AS ILE. THE RESIDUE IS ANNOTATED AS A CONFLICT IN THE SWS ENTRY AS OF 16-07-2003

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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: 2.53 Å3/Da / Density % sol: 42 %
Crystal growpH: 4.6
Details: 0.2 M AMMONIUM SULPHATE, 20% M-PEG 5K, 0.1M SODIUM ACETATE PH 4.6, 16% GLYCEROL
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Mammonium sulfate1reservoir
220 %(w/v)MPEG50001reservoir
30.1 Msodium acetate1reservoirpH4.6
410 %(w/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→45 Å / Num. obs: 26342 / % possible obs: 93.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 2.595 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / % possible all: 93.1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 16 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 93.1 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
SHARPmodel building
TNT5Frefinement
SCALAdata scaling
MOLREPphasing
BUSTERphasing
TNTphasing
SHARPphasing
DMphasing
SOLOMONphasing
SIGMAAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H03

1h03


Resolution: 2.2→25 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: BUSTER-TNT MAXIMUM LIKELIHOOD REFINEMENT ANISOTROPIC SCALING BETAIJS: BETA11:-14.4 BETA12:- 0.8 BETA13:0.3 BETA22:6.3 BETA23:4.9 BETA33:1.95
RfactorNum. reflection% reflectionSelection details
all0.211 26324 --
obs-26324 93.5 %-
Rfree---RANDOM
Solvent computationSolvent model: BABINET SCALING / Bsol: 63 Å2 / ksol: 0.45 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3930 0 80 261 4271
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00741172
X-RAY DIFFRACTIONt_angle_deg0.80155433
X-RAY DIFFRACTIONt_dihedral_angle_d19.5923800
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011102
X-RAY DIFFRACTIONt_gen_planes0.0185815
X-RAY DIFFRACTIONt_it1.2411420
X-RAY DIFFRACTIONt_nbd0.059743
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
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_contact
Refinement
*PLUS
Num. reflection Rfree: 1342 / % reflection Rfree: 5 % / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.590
X-RAY DIFFRACTIONt_planar_d0.012
X-RAY DIFFRACTIONt_plane_restr0.0185

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