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- PDB-2yby: Structure of domains 6 and 7 of the mouse complement regulator Fa... -

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Basic information

Entry
Database: PDB / ID: 2yby
TitleStructure of domains 6 and 7 of the mouse complement regulator Factor H
ComponentsCOMPLEMENT FACTOR H
KeywordsIMMUNE SYSTEM / COMPLEMENT REGULATION / INNATE IMMUNITY / INFECTION
Function / homology
Function and homology information


activation of membrane attack complex / organelle localization / mitochondrial gene expression / photoreceptor cell differentiation / retinal rod cell development / vascular associated smooth muscle cell differentiation / Regulation of Complement cascade / monocyte aggregation / retinal pigment epithelium development / regulation of complement-dependent cytotoxicity ...activation of membrane attack complex / organelle localization / mitochondrial gene expression / photoreceptor cell differentiation / retinal rod cell development / vascular associated smooth muscle cell differentiation / Regulation of Complement cascade / monocyte aggregation / retinal pigment epithelium development / regulation of complement-dependent cytotoxicity / complement component C3b binding / regulation of complement activation / mitochondrial DNA metabolic process / glomerulus development / complement activation / complement activation, alternative pathway / neuromuscular process / response to dietary excess / ATP metabolic process / visual perception / response to cytokine / kidney development / determination of adult lifespan / mitochondrion organization / platelet aggregation / heparin binding / retina development in camera-type eye / gene expression / angiogenesis / immune response / inflammatory response / axon / external side of plasma membrane / neuronal cell body / mitochondrion / extracellular space / extracellular region
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 speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsEverett, R.J. / Caesar, J.J.E. / Johnson, S.J. / Tang, C.M. / Lea, S.M.
CitationJournal: Plos Pathog. / Year: 2012
Title: Design and Evaluation of Meningococcal Vaccines Through Structure-Based Modification of Host and Pathogen Molecules.
Authors: Johnson, S. / Tan, L. / Van Der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Harding, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / ...Authors: Johnson, S. / Tan, L. / Van Der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Harding, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / Newham, L. / Staunton, D. / Ufret-Vincenty, R. / Borrow, R. / Pickering, M.C. / Lea, S.M. / Tang, C.M.
History
DepositionMar 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Mar 25, 2015Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 16, 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: COMPLEMENT FACTOR H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4472
Polymers14,3851
Non-polymers621
Water2,324129
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.620, 34.611, 107.357
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


Mass: 14385.105 Da / Num. of mol.: 1 / Fragment: DOMAINS SUSHI 6 AND 7, RESIDUES 321-444 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P06909
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 321 TO ALA
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: 1.91 Å3/Da / Density % sol: 0.28 %
Description: MOLECULAR REPLACEMENT WITH SEPARATED DOMAINS RATHER THAN WITH THE PAIR AS ANGLE DIFFERS FROM STARTING MODEL
Crystal growpH: 6 / Details: 0.2M NACL 0.1M MES PH 6.0 20% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.58→35.79 Å / Num. obs: 15809 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 22.15 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.7
Reflection shellResolution: 1.58→1.59 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
xia2RUNNING XDSdata reduction
xia2RUNNING SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W80 CHAIN A

2w80


Resolution: 1.58→29.09 Å / Cor.coef. Fo:Fc: 0.9494 / Cor.coef. Fo:Fc free: 0.9487 / SU R Cruickshank DPI: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.101 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.092
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2080. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2080. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=3.
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 820 5.2 %RANDOM
Rwork0.1901 ---
obs0.1915 15758 99.63 %-
Displacement parametersBiso mean: 25.71 Å2
Baniso -1Baniso -2Baniso -3
1--4.78 Å20 Å20 Å2
2--1.7137 Å20 Å2
3---3.0663 Å2
Refinement stepCycle: LAST / Resolution: 1.58→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 4 129 1133
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091993HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.073578HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d404SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes27HARMONIC2
X-RAY DIFFRACTIONt_gen_planes289HARMONIC5
X-RAY DIFFRACTIONt_it1993HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.25
X-RAY DIFFRACTIONt_other_torsion15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion121SEMIHARMONIC5
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_contact2205SEMIHARMONIC4
LS refinement shellResolution: 1.58→1.69 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.254 168 6.08 %
Rwork0.2028 2594 -
all0.2059 2762 -
obs--99.63 %

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