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- PDB-3k7b: The structure of the poxvirus A33 protein reveals a dimer of uniq... -

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Basic information

Entry
Database: PDB / ID: 3k7b
TitleThe structure of the poxvirus A33 protein reveals a dimer of unique C-type lectin-like domains.
ComponentsProtein A33
KeywordsVIRAL PROTEIN / C-TYPE LECTIN-LIKE DOMAIN / homodimer / POXVIRUS / EEV / EV
Function / homology
Function and homology information


host cell membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Chordopoxvirus A33R / Chordopoxvirus A33R protein / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / C-type lectin-like/link domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesVaccinia virus WR
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSu, H.P. / Garboczi, D.N.
CitationJournal: J.Virol. / Year: 2010
Title: The structure of the poxvirus A33 protein reveals a dimer of unique C-type lectin-like domains.
Authors: Su, H.P. / Singh, K. / Gittis, A.G. / Garboczi, D.N.
History
DepositionOct 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 30, 2011Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 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: Protein A33
B: Protein A33


Theoretical massNumber of molelcules
Total (without water)22,1172
Polymers22,1172
Non-polymers00
Water75742
1
A: Protein A33


Theoretical massNumber of molelcules
Total (without water)11,0591
Polymers11,0591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein A33


Theoretical massNumber of molelcules
Total (without water)11,0591
Polymers11,0591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.94, 56.32, 41.68
Angle α, β, γ (deg.)90.00, 110.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein A33


Mass: 11058.529 Da / Num. of mol.: 2 / Fragment: UNP residues 90-185 / Mutation: L118M, L140M, K123A
Source method: isolated from a genetically manipulated source
Details: refolded in vitro / Source: (gene. exp.) Vaccinia virus WR / Strain: Western Reserve (WR) / Gene: A33R, SALL3R / Plasmid: pNAN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-RIL-X / References: UniProt: P68617
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 20% PEG 8000, 10% isopropanol, 0.1M Sodium Acetate, pH 4.30, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97622 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2006
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.976221
20.976251
ReflectionResolution: 2.1→50 Å / Num. obs: 10073 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 26.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 4.4 / % possible all: 96.2

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Processing

Software
NameVersionClassification
MAR345data collection
SOLVEphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1129284.98 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 500 5 %RANDOM
Rwork0.218 ---
obs0.218 10073 97.5 %-
all-10329 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.56 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Baniso -1Baniso -2Baniso -3
1-8.91 Å20 Å23.25 Å2
2---2.08 Å20 Å2
3----6.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 0 42 1384
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 32 4.5 %
Rwork0.259 1521 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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