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- PDB-3r62: Structure of complement regulator Factor H mutant, T1184R. -

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Basic information

Entry
Database: PDB / ID: 3r62
TitleStructure of complement regulator Factor H mutant, T1184R.
ComponentsComplement factor H
KeywordsIMMUNE SYSTEM / Complement / Immunity / Repeating Sushi domain / Regulator of Complement Activation / C3d
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsMorgan, H.P. / Jiang, J. / Herbert, A.P. / Kavanagh, D. / Uhran, D. / Barlow, P.N. / Hannan, J.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Crystallographic determination of the disease-associated T1184R variant of the complement Factor H.
Authors: Morgan, H.P. / Jiang, J. / Herbert, A.P. / Kavanagh, D. / Uhran, D. / Barlow, P.N. / Hannan, J.P.
History
DepositionMar 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement factor H
B: Complement factor H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7523
Polymers29,6602
Non-polymers921
Water7,188399
1
A: Complement factor H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9222
Polymers14,8301
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement factor H


Theoretical massNumber of molelcules
Total (without water)14,8301
Polymers14,8301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.886, 52.840, 142.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Complement factor H / H factor 1


Mass: 14829.883 Da / Num. of mol.: 2 / Fragment: Complement Factor H modules 19 and 20 / Mutation: T1184R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, CFH complement factor H, HF, HF1, HF2 / Plasmid: pPICZ-alpha / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris HCl, pH 8.5 and 12% polyethylene glycol 8000 , 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
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→71.31 Å / Num. obs: 43524 / % possible obs: 100 % / Observed criterion σ(F): 1.52 / Observed criterion σ(I): 1.52 / Redundancy: 6.5 % / Rmerge(I) obs: 0.109 / Rsym value: 0.118 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.52-1.564.60.6812.10.7691100
6.81-71.315.90.08422.20.0931100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASESphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BZM

2bzm


Resolution: 1.52→42.46 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.296 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20797 2185 5 %RANDOM
Rwork0.17768 ---
obs0.17922 41260 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.333 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.52→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 6 399 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222264
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3721.9673102
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0155292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04822.762105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38615395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4651523
X-RAY DIFFRACTIONr_chiral_restr0.3050.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211796
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_it1.4551.51372
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3922257
X-RAY DIFFRACTIONr_scbond_it3.8043892
X-RAY DIFFRACTIONr_scangle_it6.3464.5837
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.523→1.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 156 -
Rwork0.306 2859 -
obs--100 %

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