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- PDB-3sw0: Structure of the C-terminal region (modules 18-20) of complement ... -

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Basic information

Entry
Database: PDB / ID: 3sw0
TitleStructure of the C-terminal region (modules 18-20) of complement regulator Factor H
ComponentsComplement factor H
KeywordsIMMUNE SYSTEM / innate immune response / Sushi domains / cofactor in the inactivation of C3b / C3b / human plasma
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / complement component C3b binding / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / complement component C3b binding / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
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
PHOSPHATE ION / Complement factor H
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMorgan, H.P. / Guariento, M. / Schmidt, C.Q. / Barlow, P.N. / Hannan, J.P.
CitationJournal: Plos One / Year: 2012
Title: Structural Analysis of the C-Terminal Region (Modules 18-20) of Complement Regulator Factor H (FH).
Authors: Morgan, H.P. / Mertens, H.D. / Guariento, M. / Schmidt, C.Q. / Soares, D.C. / Svergun, D.I. / Herbert, A.P. / Barlow, P.N. / Hannan, J.P.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Structure summary
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
X: Complement factor H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8876
Polymers21,4231
Non-polymers4635
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.970, 68.600, 77.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Complement factor H / H factor 1


Mass: 21423.273 Da / Num. of mol.: 1 / Fragment: unp residues 1046-1231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1, HF2 / Production host: Pichia pastoris (fungus) / References: UniProt: P08603
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M Sodium Acetate trihydrate, pH 4.6, 2% v/v Tacsimate, pH 4.0 (Hampton Research formulation containing: 1.8305 M Malonic acid, 0.25 M Ammonium citrate tribasic, 0.12 M Succinic acid, 0.3 ...Details: 0.1M Sodium Acetate trihydrate, pH 4.6, 2% v/v Tacsimate, pH 4.0 (Hampton Research formulation containing: 1.8305 M Malonic acid, 0.25 M Ammonium citrate tribasic, 0.12 M Succinic acid, 0.3 M DL-Malic acid, 0.4 M Sodium acetate trihydrate, 0.5 M Sodium formate, 0.16 M Ammonium tartrate dibasic and pH adjusted using NaOH) and 16% w/v polyethylene glycol 3350 as the precipitant, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 7, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45.97 Å / Num. obs: 23272 / % possible obs: 100 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8 / Redundancy: 4.1 % / Biso Wilson estimate: 24.658 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.032 / Net I/σ(I): 13.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.5 / Num. unique all: 13563 / Rsym value: 0.172 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OXU

3oxu


Resolution: 1.8→45.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.481 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 1195 5.1 %RANDOM
Rwork0.18177 ---
obs0.18394 22011 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.447 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2--1.12 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 29 171 1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221657
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9742273
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16523.41879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10515287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8581516
X-RAY DIFFRACTIONr_chiral_restr0.2190.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211289
X-RAY DIFFRACTIONr_gen_planes_other
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_mcbond_it1.5071.5987
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.69821630
X-RAY DIFFRACTIONr_scbond_it3.9213670
X-RAY DIFFRACTIONr_scangle_it6.5724.5625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 101 -
Rwork0.298 1587 -
obs--99.7 %

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