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- PDB-4b0f: Heptameric core complex structure of C4b-binding (C4BP) protein f... -

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Basic information

Entry
Database: PDB / ID: 4b0f
TitleHeptameric core complex structure of C4b-binding (C4BP) protein from human
ComponentsC4B-BINDING PROTEIN ALPHA CHAIN
KeywordsIMMUNE SYSTEM / COMPLEMENT SYSTEM
Function / homology
Function and homology information


regulation of opsonization / response to symbiotic bacterium / negative regulation of complement activation, classical pathway / T cell mediated immunity / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of protein catabolic process / blood microparticle / innate immune response / RNA binding ...regulation of opsonization / response to symbiotic bacterium / negative regulation of complement activation, classical pathway / T cell mediated immunity / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of protein catabolic process / blood microparticle / innate immune response / RNA binding / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3730 / C4b-binding protein alpha, oligomerization domain / Oligomerization domain of C4b-binding protein alpha / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
C4b-binding protein alpha chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsSchmelz, S. / Hofmeyer, T. / Kolmar, H. / Heinz, D.W.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Arranged Sevenfold: Structural Insights Into the C-Terminal Oligomerization Domain of Human C4B-Binding Protein.
Authors: Hofmeyer, T. / Schmelz, S. / Degiacomi, M.T. / Peraro, M.D. / Daneschdar, M. / Scrima, A. / Den Heuvel, J.V. / Heinz, D.W. / Kolmar, H.
History
DepositionJul 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C4B-BINDING PROTEIN ALPHA CHAIN
B: C4B-BINDING PROTEIN ALPHA CHAIN
C: C4B-BINDING PROTEIN ALPHA CHAIN
D: C4B-BINDING PROTEIN ALPHA CHAIN
E: C4B-BINDING PROTEIN ALPHA CHAIN
F: C4B-BINDING PROTEIN ALPHA CHAIN
G: C4B-BINDING PROTEIN ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7809
Polymers51,7097
Non-polymers712
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15370 Å2
ΔGint-184.4 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.850, 73.850, 204.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
12
22
32
42
52
62
72

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 546:560 )
211CHAIN B AND (RESSEQ 546:560 )
311CHAIN C AND (RESSEQ 546:560 )
411CHAIN D AND (RESSEQ 546:560 )
511CHAIN E AND (RESSEQ 546:560 )
611CHAIN F AND (RESSEQ 546:560 )
711CHAIN G AND (RESSEQ 546:560 )
112CHAIN A AND (RESSEQ 562:590 )
212CHAIN B AND (RESSEQ 562:590 )
312CHAIN C AND (RESSEQ 562:590 )
412CHAIN D AND (RESSEQ 562:590 )
512CHAIN E AND (RESSEQ 562:590 )
612CHAIN F AND (RESSEQ 562:590 )
712CHAIN G AND (RESSEQ 562:590 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
C4B-BINDING PROTEIN ALPHA CHAIN / C4B-BINDING PROTEIN CORE COMPLEX / C4BP / PROLINE-RICH PROTEIN / PRP


Mass: 7387.036 Da / Num. of mol.: 7
Fragment: C-TERMINAL OLIGOMERIZATION DOMAIN, RESIDUES 540-597
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P04003
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence details'SAGAHAG' IS THE N-TERMINAL LINKER SEQUENCE

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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: 2.68 Å3/Da / Density % sol: 54.1 % / Description: NONE
Crystal growDetails: 46.5 % (V/V) PEG 400, 5 % (V/V) MPD, 0.1 M TRIS PH. 7.3 WITH 13.7 MG/ML C4BP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 26577 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.5 % / Biso Wilson estimate: 71.53 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.8→46.496 Å / SU ML: 0.37 / σ(F): 1.54 / Phase error: 22.6 / Stereochemistry target values: MLHL
Details: RESIDUES A539-540, B539-542, C539- -542, C592-597, D539-542, E539-540, E596-597, F539-542, F596-597 AND G595-597 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2477 1326 5 %
Rwork0.2121 --
obs0.2138 26577 99.97 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.165 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6645 Å20 Å20 Å2
2---1.6645 Å20 Å2
3---3.3291 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 2 4 2941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072965
X-RAY DIFFRACTIONf_angle_d1.0173986
X-RAY DIFFRACTIONf_dihedral_angle_d17.1061176
X-RAY DIFFRACTIONf_chiral_restr0.068474
X-RAY DIFFRACTIONf_plane_restr0.005522
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A116X-RAY DIFFRACTIONPOSITIONAL
12B116X-RAY DIFFRACTIONPOSITIONAL0.036
13C116X-RAY DIFFRACTIONPOSITIONAL0.034
14D116X-RAY DIFFRACTIONPOSITIONAL0.052
15E116X-RAY DIFFRACTIONPOSITIONAL0.035
16F116X-RAY DIFFRACTIONPOSITIONAL0.079
17G116X-RAY DIFFRACTIONPOSITIONAL0.049
21A229X-RAY DIFFRACTIONPOSITIONAL
22B229X-RAY DIFFRACTIONPOSITIONAL0.065
23C229X-RAY DIFFRACTIONPOSITIONAL0.051
24D229X-RAY DIFFRACTIONPOSITIONAL0.068
25E225X-RAY DIFFRACTIONPOSITIONAL0.059
26F229X-RAY DIFFRACTIONPOSITIONAL0.054
27G229X-RAY DIFFRACTIONPOSITIONAL0.057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.34731470.31612797X-RAY DIFFRACTION100
2.9121-3.04460.28871450.30142799X-RAY DIFFRACTION100
3.0446-3.20510.28921480.24272829X-RAY DIFFRACTION100
3.2051-3.40590.27291470.24372789X-RAY DIFFRACTION100
3.4059-3.66880.21741520.21342812X-RAY DIFFRACTION100
3.6688-4.03780.23171470.20052811X-RAY DIFFRACTION100
4.0378-4.62160.20861520.16592795X-RAY DIFFRACTION100
4.6216-5.82090.22671430.20362809X-RAY DIFFRACTION100
5.8209-46.50250.27431450.20872810X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.7833 Å / Origin y: -15.6619 Å / Origin z: -1.8839 Å
111213212223313233
T0.2666 Å20.0999 Å20.0671 Å2-0.2785 Å2-0.0165 Å2--0.2792 Å2
L2.2015 °20.1679 °20.1662 °2-2.0082 °20.3685 °2--0.8437 °2
S-0.1066 Å °0.049 Å °-0.1647 Å °0.0649 Å °0.0257 Å °-0.1747 Å °0.1233 Å °0.1197 Å °0.0746 Å °
Refinement TLS groupSelection details: ALL

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