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- PDB-2ove: Crystal Structure of Recombinant Human Complement Protein C8gamma -

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Basic information

Entry
Database: PDB / ID: 2ove
TitleCrystal Structure of Recombinant Human Complement Protein C8gamma
ComponentsComplement component 8, gamma polypeptide
KeywordsTRANSPORT PROTEIN / LIGAND BINDING PROTEIN / lipocalin / beta barrel
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / complement binding / complement activation, alternative pathway / retinol binding / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / blood microparticle / killing of cells of another organism ...Terminal pathway of complement / membrane attack complex / complement binding / complement activation, alternative pathway / retinol binding / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / blood microparticle / killing of cells of another organism / protein-containing complex binding / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Complement component C8 gamma chain / Alpha-1-microglobulin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Complement component C8 gamma chain / Complement component C8 gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChiswell, B. / Lovelace, L.L. / Brannen, C. / Ortlund, E.A. / Lebioda, L. / Sodetz, J.M.
CitationJournal: Biochim.Biophys.Acta / Year: 2007
Title: Structural features of the ligand binding site on human complement protein C8gamma: A member of the lipocalin family
Authors: Chiswell, B. / Lovelace, L.L. / Brannen, C. / Ortlund, E.A. / Lebioda, L. / Sodetz, J.M.
History
DepositionFeb 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 component 8, gamma polypeptide


Theoretical massNumber of molelcules
Total (without water)20,3201
Polymers20,3201
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.227, 59.775, 71.901
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Complement component 8, gamma polypeptide / Complement Protein C8gamma


Mass: 20320.004 Da / Num. of mol.: 1 / Mutation: Y83W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C8G / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: Q14CU0, UniProt: P07360*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 44.89 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M sodium citrate and 25-27% PEG 4000, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98925 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 16, 2003
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98925 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 12901 / Num. obs: 12610 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.046 / Χ2: 1.043 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 8.5 / Num. unique all: 1188 / Χ2: 0.775 / % possible all: 95

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
SBC-Collect19IDdata collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→500 Å / FOM work R set: 0.84 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.26 1269 9.9 %
Rwork0.226 --
obs-12321 96.1 %
Solvent computationBsol: 54.275 Å2
Displacement parametersBiso mean: 30.243 Å2
Baniso -1Baniso -2Baniso -3
1-2.468 Å20 Å20 Å2
2--5.921 Å20 Å2
3----8.389 Å2
Refinement stepCycle: LAST / Resolution: 2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 0 119 1375
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.148
X-RAY DIFFRACTIONc_mcbond_it1.9241.5
X-RAY DIFFRACTIONc_scbond_it2.3592
X-RAY DIFFRACTIONc_mcangle_it3.2452
X-RAY DIFFRACTIONc_scangle_it3.6922.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2-2.030.33400.233410450
2.03-2.060.273680.241389457
2.06-2.090.273490.239429478
2.09-2.120.259550.222409464
2.12-2.150.249540.227432486
2.15-2.190.288450.228435480
2.19-2.230.245510.232437488
2.23-2.270.223440.212432476
2.27-2.320.253470.198438485
2.32-2.370.299480.237437485
2.37-2.430.26530.237437490
2.43-2.490.328440.252457501
2.49-2.550.243580.244433491
2.55-2.630.382340.245477511
2.63-2.710.266430.255455498
2.71-2.810.226570.219449506
2.81-2.920.295580.222433491
2.92-3.060.255510.229438489
3.06-3.220.26530.223457510
3.22-3.420.26470.228456503
3.42-3.680.193530.208453506
3.68-4.050.253500.224462512
4.05-4.640.273500.213462512
4.64-5.850.248580.202464522
5.85-500.010.267590.254471530
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramHicupCNS_TOPPAR:protein.topHIcup
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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