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- PDB-3zd1: STRUCTURE OF THE TWO C-TERMINAL DOMAINS OF COMPLEMENT FACTOR H RE... -

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Entry
Database: PDB / ID: 3zd1
TitleSTRUCTURE OF THE TWO C-TERMINAL DOMAINS OF COMPLEMENT FACTOR H RELATED PROTEIN 2
ComponentsCOMPLEMENT FACTOR H-RELATED PROTEIN 2
KeywordsIMMUNE SYSTEM / CFHR-2 / CFHR2 / FHR2
Function / homology
Function and homology information


complement component C3b binding / complement activation / cytolysis by host of symbiont cells / negative regulation of protein binding / Regulation of Complement cascade / protein-containing complex / extracellular space / 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
Complement factor H-related protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCaesar, J.J.E. / Goicoechea de Jorge, E. / Pickering, M.C. / Lea, S.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Dimerization of Complement Factor H-Related Proteins Modulates Complement Activation in Vivo.
Authors: Goicoechea De Jorge, E. / Caesar, J.J.E. / Malik, T.H. / Patel, M. / Colledge, M. / Johnson, S. / Hakobyan, S. / Morgan, B.P. / Harris, C.L. / Pickering, M.C. / Lea, S.M.
History
DepositionNov 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Dec 20, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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-RELATED PROTEIN 2
B: COMPLEMENT FACTOR H-RELATED PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,22712
Polymers28,6062
Non-polymers62110
Water1,38777
1
A: COMPLEMENT FACTOR H-RELATED PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6767
Polymers14,3031
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COMPLEMENT FACTOR H-RELATED PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5525
Polymers14,3031
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.950, 25.180, 95.680
Angle α, β, γ (deg.)90.00, 93.80, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.996773, -0.016503, -0.078563), (0.019391, 0.999158, 0.036146), (0.0779, -0.037553, 0.996254)
Vector: -2.036, 11.902, 45.204)

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Components

#1: Protein COMPLEMENT FACTOR H-RELATED PROTEIN 2 / FHR-2 / DDESK59 / H FACTOR-LIKE 3 / H FACTOR-LIKE PROTEIN 2


Mass: 14303.232 Da / Num. of mol.: 2 / Fragment: SCR DOMAINS 3 AND 4, RESIDUES 147-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36980
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.96 % / Description: NONE
Crystal growDetails: 30% (W/V) PEG 8000, 0.2M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2011 / Details: MIRRORS
RadiationMonochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2→95.47 Å / Num. obs: 16993 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 27.21 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4 / % possible all: 86.8

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G7I

2g7i


Resolution: 2→19.09 Å / Cor.coef. Fo:Fc: 0.9283 / Cor.coef. Fo:Fc free: 0.9205 / SU R Cruickshank DPI: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.213 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.24 859 5.06 %RANDOM
Rwork0.2106 ---
obs0.2121 16963 96.14 %-
Displacement parametersBiso mean: 27.45 Å2
Baniso -1Baniso -2Baniso -3
1--2.0665 Å20 Å2-5.2159 Å2
2--0.2685 Å20 Å2
3---1.798 Å2
Refine analyzeLuzzati coordinate error obs: 0.241 Å
Refinement stepCycle: LAST / Resolution: 2→19.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 40 77 2069
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012040HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.12752HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d694SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes280HARMONIC5
X-RAY DIFFRACTIONt_it2040HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion16.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion254SEMIHARMONIC5
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_contact2294SEMIHARMONIC4
LS refinement shellResolution: 2→2.12 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2741 132 5.14 %
Rwork0.209 2435 -
all0.2122 2567 -
obs--96.14 %

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