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- PDB-6th1: IE1 from rat cytomegalovirus -

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Basic information

Entry
Database: PDB / ID: 6th1
TitleIE1 from rat cytomegalovirus
ComponentsImmediate early protein 1
KeywordsVIRAL PROTEIN / RCMV IE1
Function / homologyImmediate early protein 1
Function and homology information
Biological speciesMurid betaherpesvirus 2 (Rat cytomegalovirus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.4 Å
AuthorsSchweininger, J. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB796 Germany
CitationJournal: Plos Pathog. / Year: 2021
Title: Cytomegalovirus immediate-early 1 proteins form a structurally distinct protein class with adaptations determining cross-species barriers.
Authors: Schweininger, J. / Scherer, M. / Rothemund, F. / Schilling, E.M. / Worz, S. / Stamminger, T. / Muller, Y.A.
History
DepositionNov 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain ..._entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Sep 15, 2021Group: Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / database_2 / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Immediate early protein 1


Theoretical massNumber of molelcules
Total (without water)40,8671
Polymers40,8671
Non-polymers00
Water00
1
R: Immediate early protein 1

R: Immediate early protein 1


Theoretical massNumber of molelcules
Total (without water)81,7352
Polymers81,7352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area4470 Å2
ΔGint-22 kcal/mol
Surface area36410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.049, 173.049, 134.485
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Immediate early protein 1


Mass: 40867.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid betaherpesvirus 2 (Rat cytomegalovirus)
Gene: IE / Production host: Escherichia coli (E. coli) / References: UniProt: O57046

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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: 7.11 Å3/Da / Density % sol: 82.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: TRIS/HCl, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 20, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.38→18.776 Å / Num. obs: 16925 / % possible obs: 99 % / Redundancy: 79.385 % / Biso Wilson estimate: 132 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.359 / Rrim(I) all: 0.361 / Χ2: 1.054 / Net I/σ(I): 19.08 / Num. measured all: 1343584
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.38-3.5980.5875.6531.02210331268426100.3385.68897.2
3.59-3.8384.0912.8422.38212665253225290.7832.85999.9
3.83-4.1482.671.3795.04195018235923590.9551.388100
4.14-4.5381.0330.6899.87178191219921990.9850.693100
4.53-5.0673.7990.40415.67145088200019660.9920.40798.3
5.06-5.8381.3710.41315.97143701178617660.9940.41698.9
5.83-7.1180.4320.24127.15123142153115310.9980.242100
7.11-9.9571.1360.05980.42862881230121310.05998.6
9.95-18.77665.3720.042109.794916077875210.04296.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
HKL2Mapphasing
RefinementMethod to determine structure: MAD / Resolution: 3.4→18.776 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2442 1626 9.8 %
Rwork0.215 14964 -
obs0.2179 16590 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 218.28 Å2 / Biso mean: 130.2635 Å2 / Biso min: 81.69 Å2
Refinement stepCycle: final / Resolution: 3.4→18.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 0 0 2799
Num. residues----360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4-3.49950.37591350.3592117996
3.4995-3.61160.31721200.32431251100
3.6116-3.73980.3391460.2971212100
3.7398-3.88820.24181170.26711242100
3.8882-4.06350.26511330.25171258100
4.0635-4.27530.24851360.21481226100
4.2753-4.53960.21471490.20941234100
4.5396-4.88440.19681420.19141249100
4.8844-5.36550.2721350.2193120796
5.3655-6.11830.32341320.26081277100
6.1183-7.62170.28031490.23781287100
7.6217-18.7760.17911320.1515134298
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.03470.34480.1192-0.30240.27670.0445-1.02070.5368-0.5802-0.01520.04920.12240.2091-0.23171.15380.1171-0.01011.4643-0.18711.45257.902957.901541.7066
20.77410.20530.08560.2047-0.2211-0.7389-0.04210.6966-0.1286-0.0362-0.14150.1906-0.2233-0.52421.00050.29370.01351.28320.01830.958259.758669.356138.0647
30.39990.1054-0.3304-0.01950.12220.5335-0.00770.0044-0.1439-0.05710.07090.0498-0.35990.05770.93130.03620.00471.0239-0.04890.98787.327358.830925.1602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'R' and (resid 33 through 67 )R33 - 67
2X-RAY DIFFRACTION2chain 'R' and (resid 68 through 165 )R68 - 165
3X-RAY DIFFRACTION3chain 'R' and (resid 166 through 392 )R166 - 392

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