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- PDB-2cme: The crystal structure of SARS coronavirus ORF-9b protein -

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Basic information

Entry
Database: PDB / ID: 2cme
TitleThe crystal structure of SARS coronavirus ORF-9b protein
Components(HYPOTHETICAL PROTEIN ...) x 4
KeywordsHYPOTHETICAL PROTEIN / ALTERNATIVE OPEN READING FRAME / LIPID-BINDING / VIRUS ASSEMBLY
Function / homology
Function and homology information


virion component => GO:0044423 / Translation of Replicase and Assembly of the Replication Transcription Complex / host cell endoplasmic reticulum / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell cytoplasmic vesicle membrane / host cell nucleus / membrane / identical protein binding
Similarity search - Function
Protein 9b, Betacoronavirus / Protein 9b, SARS-CoV / Betacoronavirus lipid binding protein / Sarbecovirus 9b domain profile.
Similarity search - Domain/homology
DECANE / ORF9b protein
Similarity search - Component
Biological speciesHUMAN SARS CORONAVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMeier, C. / Aricescu, A.R. / Assenberg, R. / Aplin, R.T. / Gilbert, R.J.C. / Grimes, J.M. / Stuart, D.I.
CitationJournal: Structure / Year: 2006
Title: The Crystal Structure of Orf-9B, a Lipid Binding Protein from the Sars Coronavirus.
Authors: Meier, C. / Aricescu, A.R. / Assenberg, R. / Aplin, R.T. / Gilbert, R.J.C. / Grimes, J.M. / Stuart, D.I.
History
DepositionMay 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN 5
B: HYPOTHETICAL PROTEIN 5
C: HYPOTHETICAL PROTEIN 5
D: HYPOTHETICAL PROTEIN 5
E: HYPOTHETICAL PROTEIN 5
F: HYPOTHETICAL PROTEIN 5
G: HYPOTHETICAL PROTEIN 5
H: HYPOTHETICAL PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,63112
Polymers68,0628
Non-polymers5694
Water1267
1
A: HYPOTHETICAL PROTEIN 5
B: HYPOTHETICAL PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4813
Polymers17,3392
Non-polymers1421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: HYPOTHETICAL PROTEIN 5
D: HYPOTHETICAL PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9843
Polymers16,8422
Non-polymers1421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: HYPOTHETICAL PROTEIN 5
F: HYPOTHETICAL PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0833
Polymers16,9412
Non-polymers1421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: HYPOTHETICAL PROTEIN 5
H: HYPOTHETICAL PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0833
Polymers16,9412
Non-polymers1421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)140.028, 140.028, 45.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.34249, -0.55537, 0.7578), (-0.59135, -0.49934, -0.63321), (0.73007, -0.665, -0.1574)
Vector: 68.8237, 72.195, -4.6497)

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Components

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HYPOTHETICAL PROTEIN ... , 4 types, 8 molecules ABCDFHEG

#1: Protein HYPOTHETICAL PROTEIN 5 / Hypothesis / ORF-9B / ORF13


Mass: 8591.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN SARS CORONAVIRUS / Strain: HKU-39849 / Cell line: VERO E6 / Plasmid: GATEWAY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA PLYSS / References: UniProt: P59636
#2: Protein HYPOTHETICAL PROTEIN 5 / Hypothesis / ORF-9B / ORF13


Mass: 8748.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CONTAINS LIPID MOLECULE (MODELLED AS DECANE, RESIDUE NAME D10)
Source: (gene. exp.) HUMAN SARS CORONAVIRUS / Strain: HKU-39849 / Cell line: VERO E6 / Plasmid: GATEWAY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA PLYSS / References: UniProt: P59636
#3: Protein
HYPOTHETICAL PROTEIN 5 / Hypothesis / ORF-9B / ORF13


Mass: 8420.795 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CONTAINS LIPID MOLECULE (MODELLED AS DECANE, RESIDUE NAME D10)
Source: (gene. exp.) HUMAN SARS CORONAVIRUS / Strain: HKU-39849 / Cell line: VERO E6 / Plasmid: GATEWAY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA PLYSS / References: UniProt: P59636
#4: Protein HYPOTHETICAL PROTEIN 5 / Hypothesis / ORF-9B / ORF13


Mass: 8519.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN SARS CORONAVIRUS / Strain: HKU-39849 / Cell line: VERO E6 / Plasmid: GATEWAY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA PLYSS / References: UniProt: P59636

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Non-polymers , 2 types, 11 molecules

#5: Chemical
ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growpH: 8.2
Details: 32% PEG3350, 200MM MGCL2, 100MM TRIS-HCL PH8.2, pH 8.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97903
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 9, 2004 / Details: MIRRORS
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.8→19.9 Å / Num. obs: 22040 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14.9 % / Biso Wilson estimate: 84 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 22.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 15.1 % / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.9 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: RESIDUAL
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1763 8 %RANDOM
Rwork0.266 ---
obs0.266 22028 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.441 Å20 Å20 Å2
2--4.441 Å20 Å2
3----8.881 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 40 7 4824
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.8874
X-RAY DIFFRACTIONc_mcangle_it10.196
X-RAY DIFFRACTIONc_scbond_it7.9395
X-RAY DIFFRACTIONc_scangle_it12.76210
Refine LS restraints NCSRms dev Biso : 0.2722 Å2 / Rms dev position: 0.2136 Å / Weight Biso : 3 / Weight position: 40
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.432 -8 %
Rwork0.404 2715 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3DECANE.PARAMDECANE.TOP

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