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- PDB-3erb: The Crystal Structure of C2b, a Fragment of Complement Component ... -

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Basic information

Entry
Database: PDB / ID: 3erb
TitleThe Crystal Structure of C2b, a Fragment of Complement Component C2 produced during C3-convertase Formation
ComponentsComplement C2Complement component 2
KeywordsHYDROLASE / Complement component C2b / C3/C5 convertase / complement control protein (CCP) / short consensus repeat(SCR) / Sushi domain / human complement system / complement second component C2 / Complement pathway / Disease mutation / Glycoprotein / Immune response / Innate immunity / Polymorphism / Protease / Secreted / Serine protease / Sushi
Function / homology
Function and homology information


classical-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / complement activation, classical pathway / response to nutrient / Regulation of Complement cascade ...classical-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / complement activation, classical pathway / response to nutrient / Regulation of Complement cascade / response to bacterium / response to lipopolysaccharide / serine-type endopeptidase activity / innate immune response / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
Complement B/C2 / 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 / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain ...Complement B/C2 / 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 / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNarayan, S.V.L. / Krishnan, V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: The structure of C2b, a fragment of complement component C2 produced during C3 convertase formation
Authors: Krishnan, V. / Xu, Y. / Macon, K. / Volanakis, J.E. / Narayana, S.V.
History
DepositionOct 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C2


Theoretical massNumber of molelcules
Total (without water)23,7081
Polymers23,7081
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.060, 60.060, 61.687
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Complement C2 / Complement component 2 / C3/C5 convertase / Complement C2b fragment


Mass: 23707.523 Da / Num. of mol.: 1 / Fragment: Complement C2b fragment, N-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High Five(BTI-TN-5B1-4) / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P06681, classical-complement-pathway C3/C5 convertase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 3350, 0.22M Sodium Chloride, 0.02M Betaine Hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 23095 / % possible obs: 100 % / Redundancy: 4.36 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.15 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNSrefinement
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OK5

2ok5


Resolution: 1.8→21.52 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.49 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23963 1182 5.1 %RANDOM
Rwork0.2142 ---
obs0.21552 21882 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.257 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 0 197 1612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211463
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9511996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.16322.96964
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19815206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7081512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021167
X-RAY DIFFRACTIONr_nbd_refined0.2030.2666
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.217
X-RAY DIFFRACTIONr_mcbond_it0.8131.5963
X-RAY DIFFRACTIONr_mcangle_it1.15721502
X-RAY DIFFRACTIONr_scbond_it2.073585
X-RAY DIFFRACTIONr_scangle_it3.3414.5493
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 98 -
Rwork0.321 1627 -
obs--99.94 %

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