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- PDB-4wic: Immediate-early 1 protein (IE1) of rhesus macaque cytomegalovirus -

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Basic information

Entry
Database: PDB / ID: 4wic
TitleImmediate-early 1 protein (IE1) of rhesus macaque cytomegalovirus
ComponentsRhUL123
KeywordsVIRAL PROTEIN / Cytomegalovirus / antagonist / all-alpha
Function / homologyCytomegalovirus IE1/IE2 / Cytomegalovirus IE1 protein / : / DNA-templated viral transcription / RhUL123
Function and homology information
Biological speciesMacacine herpesvirus 3 (Rhesus cytomegalovirus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsKlingl, S. / Scherer, M. / Sevvana, M. / Muller, Y.A. / Stamminger, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB796 Germany
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Controlled crystal dehydration triggers a space-group switch and shapes the tertiary structure of cytomegalovirus immediate-early 1 (IE1) protein.
Authors: Klingl, S. / Scherer, M. / Stamminger, T. / Muller, Y.A.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: RhUL123
B: RhUL123
C: RhUL123
D: RhUL123


Theoretical massNumber of molelcules
Total (without water)168,5824
Polymers168,5824
Non-polymers00
Water0
1
A: RhUL123
B: RhUL123


Theoretical massNumber of molelcules
Total (without water)84,2912
Polymers84,2912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-17 kcal/mol
Surface area35880 Å2
MethodPISA
2
C: RhUL123
D: RhUL123


Theoretical massNumber of molelcules
Total (without water)84,2912
Polymers84,2912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-17 kcal/mol
Surface area36010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.950, 278.550, 61.620
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RhUL123


Mass: 42145.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macacine herpesvirus 3 (Rhesus cytomegalovirus)
Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2FAE9

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Reservoir 700 microL: 15 % (w/v) PEG 3350, 400 mM magnesium formate Drop ratio: 1 to 2 microL protein solution (20 mg/mL) plus 1 microL of reservoir solution supplemented with microseeds

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184, 1.0402, 1.0372, 1.0346, 0.9797
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 16, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
21.04021
31.03721
41.03461
50.97971
ReflectionResolution: 2.85→20 Å / Num. all: 45141 / Num. obs: 45137 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 70.08 Å2 / Net I/σ(I): 16.9
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 1.7 % / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.85→19.935 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 31.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 2270 5.03 %
Rwork0.2117 --
obs0.2142 45129 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.6 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11177 0 0 0 11177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111340
X-RAY DIFFRACTIONf_angle_d1.43815237
X-RAY DIFFRACTIONf_dihedral_angle_d14.8444396
X-RAY DIFFRACTIONf_chiral_restr0.0611755
X-RAY DIFFRACTIONf_plane_restr0.0071943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-2.91190.40591290.32362714X-RAY DIFFRACTION100
2.9119-2.97940.38961360.31092630X-RAY DIFFRACTION100
2.9794-3.05360.34371620.28972698X-RAY DIFFRACTION100
3.0536-3.13590.32891250.29532638X-RAY DIFFRACTION100
3.1359-3.22780.35261650.28362697X-RAY DIFFRACTION100
3.2278-3.33150.35681470.26442628X-RAY DIFFRACTION100
3.3315-3.450.25821490.25022683X-RAY DIFFRACTION100
3.45-3.58740.30291270.24372712X-RAY DIFFRACTION100
3.5874-3.74960.30361490.23032622X-RAY DIFFRACTION100
3.7496-3.94590.27081200.21562720X-RAY DIFFRACTION100
3.9459-4.1910.27761340.20182709X-RAY DIFFRACTION100
4.191-4.51110.21951250.18562685X-RAY DIFFRACTION100
4.5111-4.95870.23391430.18592670X-RAY DIFFRACTION100
4.9587-5.66180.28971510.20692699X-RAY DIFFRACTION100
5.6618-7.07980.25881560.22922674X-RAY DIFFRACTION100
7.0798-19.93530.15531520.1382680X-RAY DIFFRACTION99

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