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- PDB-1ypy: Crystal Structure of Vaccinia Virus L1 protein -

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Basic information

Entry
Database: PDB / ID: 1ypy
TitleCrystal Structure of Vaccinia Virus L1 protein
ComponentsVirion membrane protein
KeywordsVIRAL PROTEIN / Vaccinia virus / Orthopox / Variola virus / smallpox / L1
Function / homologyVirion membrane protein, poxvirus L1-related / Lipid membrane protein of large eukaryotic DNA viruses / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane / Entry-fusion complex associated protein OPG095
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.51 Å
AuthorsSu, H.P. / Garman, S.C. / Allison, T.J. / Fogg, C. / Moss, B. / Garboczi, D.N.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: The 1.51-Angstrom structure of the poxvirus L1 protein, a target of potent neutralizing antibodies.
Authors: Su, H.P. / Garman, S.C. / Allison, T.J. / Fogg, C. / Moss, B. / Garboczi, D.N.
History
DepositionJan 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 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 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Virion membrane protein
B: Virion membrane protein


Theoretical massNumber of molelcules
Total (without water)39,0662
Polymers39,0662
Non-polymers00
Water5,891327
1
A: Virion membrane protein


Theoretical massNumber of molelcules
Total (without water)19,5331
Polymers19,5331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Virion membrane protein


Theoretical massNumber of molelcules
Total (without water)19,5331
Polymers19,5331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.746, 56.627, 72.557
Angle α, β, γ (deg.)90.00, 129.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Virion membrane protein


Mass: 19532.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Gene: L1 / Plasmid: pLM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-CodonPlus-RIL / References: UniProt: P07612
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.244.1
22.244.2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop8PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP
2932vapor diffusion, hanging drop8PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11
SYNCHROTRONAPS 19-ID20.97702
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJun 3, 2003
ADSC QUANTUM 42CCDJul 4, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.977021
ReflectionNumber: 15507
ReflectionResolution: 1.51→50 Å / Num. obs: 52912 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.058 / Net I/σ(I): 12.3
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.55 / Num. unique all: 5290 / Χ2: 1.045 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-13.10328.27122.475SE19.30.54
267.34926.56325.998SE13.60.42
372.81923.8613.845SE290.54
479.9869.6173.523SE510.67
56.57214.8326.083SE55.90.52
646.8424.284.178SE51.70.4
Phasing dmFOM : 0.74 / FOM acentric: 0.76 / FOM centric: 0.57 / Reflection: 6895 / Reflection acentric: 6398 / Reflection centric: 497
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.6-19.9580.880.880.5829524253
5.4-8.60.780.810.57940838102
4.3-5.40.810.830.581171108388
3.8-4.30.80.810.621153107479
3.2-3.80.730.740.5920631951112
3-3.20.60.610.431273121063

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.06phasing
CNS1.1refinement
MAR345data collection
RefinementMethod to determine structure: SAD / Resolution: 1.51→50 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The close contact between B5 (CB ALA) and B82 (CG GLU) may indicate flexibility in side chain of B82 as well as the disorder in B5, which is the n-terminus in that molecule. It is possible ...Details: The close contact between B5 (CB ALA) and B82 (CG GLU) may indicate flexibility in side chain of B82 as well as the disorder in B5, which is the n-terminus in that molecule. It is possible that there are alternate positions in both residues to support packing between the asymmetric units at this interface, but the model is the best fit that did not violate geometric requirements.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2646 4.9 %Random
Rwork0.239 ---
all0.239 ---
obs0.239 52902 98.7 %-
Displacement parametersBiso mean: 58.345 Å2
Baniso -1Baniso -2Baniso -3
1--0.512 Å20 Å21.403 Å2
2---2.082 Å20 Å2
3---2.594 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 0 327 2940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.076
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.15
LS refinement shellResolution: 1.51→1.6 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.322 460 -
Rwork0.284 --
obs-8201 97.7 %

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