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- PDB-2ovd: Crystal Structure of Human Complement Protein C8gamma with Laurate -

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Basic information

Entry
Database: PDB / ID: 2ovd
TitleCrystal Structure of Human Complement Protein C8gamma with Laurate
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 protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
LAURIC ACID / Complement component C8 gamma chain / Complement component C8 gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 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 / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement component 8, gamma polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5202
Polymers20,3201
Non-polymers2001
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.081, 59.539, 70.836
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
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: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M sodium citrate and 25-27% PEG 4000. Sodium laurate (Sigma) was solubilized in methanol/water and used to prepare a 0.9 mM solution in 0.1M imidazole containing 32% PEG 4000, pH 7.0, pH ...Details: 0.1 M sodium citrate and 25-27% PEG 4000. Sodium laurate (Sigma) was solubilized in methanol/water and used to prepare a 0.9 mM solution in 0.1M imidazole containing 32% PEG 4000, pH 7.0, 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-ID / Wavelength: 0.91963 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2004
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91963 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 18059 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.058 / Χ2: 0.863 / Net I/σ(I): 10.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1412 / Χ2: 0.744 / % possible all: 77.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
SBC-Collect19IDdata collection
HKL-2000data reduction
CNSphasing
RefinementResolution: 1.8→500 Å / FOM work R set: 0.889 / σ(F): 1149
RfactorNum. reflection% reflection
Rfree0.23 1516 8.9 %
Rwork0.208 --
obs-15376 89.9 %
Solvent computationBsol: 56.68 Å2
Displacement parametersBiso mean: 25.504 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2--3.164 Å20 Å2
3----1.344 Å2
Refinement stepCycle: LAST / Resolution: 1.8→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 14 199 1469
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.153
X-RAY DIFFRACTIONc_mcbond_it2.0831.5
X-RAY DIFFRACTIONc_scbond_it2.6372
X-RAY DIFFRACTIONc_mcangle_it3.4712
X-RAY DIFFRACTIONc_scangle_it4.1542.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.8-1.820.247360.22275311
1.82-1.840.194220.216308330
1.84-1.860.195290.201372401
1.86-1.890.205340.216377411
1.89-1.910.245620.22387449
1.91-1.940.221500.201383433
1.94-1.970.227510.19462513
1.97-20.255500.213450500
2-2.030.208350.202463498
2.03-2.060.224530.203458511
2.06-2.10.249470.213474521
2.1-2.130.258360.203490526
2.13-2.180.265390.215462501
2.18-2.220.235610.199480541
2.22-2.270.251550.196465520
2.27-2.320.207570.189479536
2.32-2.380.191570.201478535
2.38-2.440.221550.19480535
2.44-2.510.243600.203473533
2.51-2.60.263540.202484538
2.6-2.690.23520.222493545
2.69-2.80.253460.212517563
2.8-2.920.231490.197489538
2.92-3.080.279510.221521572
3.08-3.270.201640.185489553
3.27-3.520.255580.21522580
3.52-3.880.194620.196515577
3.88-4.440.223560.204521577
4.44-5.590.217680.204536604
5.59-500.010.245670.257557624
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
X-RAY DIFFRACTION5ligand.paramligand.top

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