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- PDB-4e9o: Vaccinia D8L ectodomain structure -

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Basic information

Entry
Database: PDB / ID: 4e9o
TitleVaccinia D8L ectodomain structure
ComponentsIMV membrane protein
KeywordsVIRAL PROTEIN / CAH alpha fold / Vp7 motif / beta sheet / cell surface chondroitin binding / viral entry / chondroitin sulfate
Function / homology
Function and homology information


carbonate dehydratase activity / virion membrane / zinc ion binding / membrane
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Cell surface-binding protein OPG105
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsMatho, M.H. / Zajonc, D.M.
CitationJournal: J.Virol. / Year: 2012
Title: Structural and Biochemical Characterization of the Vaccinia Virus Envelope Protein D8 and Its Recognition by the Antibody LA5.
Authors: Matho, M.H. / Maybeno, M. / Benhnia, M.R. / Becker, D. / Meng, X. / Xiang, Y. / Crotty, S. / Peters, B. / Zajonc, D.M.
History
DepositionMar 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
X: IMV membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,84413
Polymers31,3211
Non-polymers1,52312
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.281, 71.281, 44.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein IMV membrane protein / D8L antigen


Mass: 31321.184 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 1-261)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Acambis clone 2000 / Gene: VACAC2_124, VACCL3_124, VAC_DPP17_124 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus BL21 / References: UniProt: Q1M1K6
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 1.8 Å3/Da / Density % sol: 31.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2 M sodium iodide, 20% PEG3350, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.100002 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2011 / Details: mirrors
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.100002 Å / Relative weight: 1
ReflectionResolution: 1.42→25.9 Å / Num. all: 40635 / Num. obs: 40635 / % possible obs: 99.3675 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.068 / Net I/σ(I): 33.6
Reflection shellResolution: 1.42→1.45 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2880 / Rsym value: 0.63 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ETQ

4etq


Resolution: 1.42→25.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.241 / SU ML: 0.044 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.18987 1313 3.1 %RANDOM
Rwork0.17381 ---
obs0.17434 40635 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.471 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.42→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 12 206 2085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222030
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9522786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21625.15597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77715353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.823154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211571
X-RAY DIFFRACTIONr_mcbond_it0.7851.51214
X-RAY DIFFRACTIONr_mcangle_it1.39921994
X-RAY DIFFRACTIONr_scbond_it2.0983816
X-RAY DIFFRACTIONr_scangle_it3.2414.5776
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 98 -
Rwork0.249 2971 -
obs-2880 99.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.19530.8854-0.97922.6957-0.89040.99360.21660.11790.51020.13020.00220.1973-0.2171-0.1023-0.21880.10280.02580.02380.0470.01640.073119.576411.1615-3.7079
22.3366-0.36370.11421.3407-0.51971.75460.04120.11520.0541-0.03680.01950.0149-0.0642-0.0586-0.06070.01430.00670.01410.00310.00770.022219.90796.0518-2.2989
31.21380.0194-0.2551.3471-0.15251.41210.03070.0079-0.01430.0074-0.0019-0.05250.033-0.0004-0.02880.00370.001-0.0120.0275-0.00960.016424.27222.66330.394
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X3 - 40
2X-RAY DIFFRACTION2X41 - 132
3X-RAY DIFFRACTION3X133 - 234

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