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- PDB-4osn: Crystal structure of engineered HCMV glycoprotein B Domain II -

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Basic information

Entry
Database: PDB / ID: 4osn
TitleCrystal structure of engineered HCMV glycoprotein B Domain II
ComponentsEnvelope glycoprotein B
KeywordsVIRAL PROTEIN / PH domain / antigenic domain / fusion protein / viral envelope
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / PH-domain like - #100 / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily ...Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / PH-domain like - #100 / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / PH-domain like / Roll / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDiestel, U. / Muller, Y.A.
CitationJournal: To be Published
Title: Crystal structure of engineered HCMV glycoprotein B Domain II
Authors: Diestel, U. / Muller, Y.A.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein B


Theoretical massNumber of molelcules
Total (without water)14,5121
Polymers14,5121
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.922, 89.922, 75.654
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

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Components

#1: Protein Envelope glycoprotein B / gB / Glycoprotein GP55


Mass: 14512.166 Da / Num. of mol.: 1 / Fragment: UNP residues 113-132, 344-438
Source method: isolated from a genetically manipulated source
Details: ARTIFICIAL 4-RESIDUE LINKER AGSG BETWEEN RESIDUES 132 AND 344
Source: (gene. exp.) Human cytomegalovirus / Strain: Towne / Gene: gB, UL55 / Production host: Escherichia coli (E. coli) / References: UniProt: P13201
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M Lithium Sulfate, 0.1M Na-HEPES salt, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 15, 2011
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.76→34.03 Å / Num. obs: 18070 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3
Reflection shellResolution: 1.76→1.81 Å / % possible all: 97.2

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Processing

Software
NameVersionClassification
mxCuBEdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→34.03 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.345 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 906 5 %RANDOM
Rwork0.20206 ---
obs0.20337 17163 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.609 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.53 Å20 Å2
2--0.53 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.76→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 0 74 961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02991
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9211350
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6225.19252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3515186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.82155
X-RAY DIFFRACTIONr_chiral_restr0.110.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02763
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0931.414473
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8562.628596
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6911.654517
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.677.7641542
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 65 -
Rwork0.268 1228 -
obs--97.22 %
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)
18.06161.2835-3.21875.1136-1.37474.5975-0.2528-0.6001-0.15480.61380.02310.0281-0.14660.38470.22970.3069-0.0081-0.02720.1210.03430.1117-41.66414.1082.688
25.43751.1371-0.50963.7313-1.08732.4269-0.3583-0.30560.03320.61550.18910.2002-0.33530.23080.16920.3308-0.01040.0330.10780.01980.108-43.86916.2111.647
32.1985-2.07393.24197.7629-7.5099.28510.2498-0.16580.06890.9835-0.3959-0.1124-0.52360.41950.14610.3608-0.1543-0.06460.18590.01310.1037-36.78117.1255.579
42.12670.09150.04643.7057-1.66732.5946-0.14810.0318-0.04020.09940.19050.3654-0.13070.0548-0.04240.1787-0.0168-0.00310.06070.00990.1173-46.5547.146-4.266
53.76371.11780.08232.82630.40925.91010.0714-0.129-0.01330.2967-0.0706-0.0422-0.30890.3231-0.00070.2644-0.028-0.00060.10060.03040.0955-40.4710.6310.995
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A118 - 344
2X-RAY DIFFRACTION2A345 - 360
3X-RAY DIFFRACTION3A361 - 381
4X-RAY DIFFRACTION4A382 - 417
5X-RAY DIFFRACTION5A418 - 437

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