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- PDB-6vpe: Crystal structure of transcriptional regulator from bacteriophage 186 -

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Basic information

Entry
Database: PDB / ID: 6vpe
TitleCrystal structure of transcriptional regulator from bacteriophage 186
ComponentsRegulatory protein CII
KeywordsGENE REGULATION / DNA binding transcriptional regulator from bacteriophage 186
Function / homologyBacteriophage 186, CII-like / Phage regulatory protein CII (CP76) / DNA binding / IODIDE ION / Regulatory protein CII
Function and homology information
Biological speciesEscherichia phage 186 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.211 Å
AuthorsTruong, J.Q. / Panjikar, S. / Bruning, J.B. / Shearwin, K.E.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP150103009 Australia
Australian Research Council (ARC)DP160101450 Australia
CitationJournal: To Be Published
Title: Crystal structure of a transcriptional regulator from bacteriophage 186
Authors: Truong, J.Q. / Pukala, T. / Panjikar, S. / Bruning, J.B. / Shearwin, K.S.
History
DepositionFeb 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein CII
B: Regulatory protein CII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7768
Polymers37,0142
Non-polymers7616
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-56 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.860, 46.140, 38.310
Angle α, β, γ (deg.)90.000, 99.420, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Regulatory protein CII


Mass: 18507.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage 186 (virus) / Gene: CII, CP76 / Production host: Escherichia coli (E. coli) / References: UniProt: P21678
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 2 M ammonium sulfate, 0.1 M Bis-Tris:HCl, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.4586 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.21→44.45 Å / Num. obs: 14298 / % possible obs: 97.8 % / Redundancy: 7 % / Biso Wilson estimate: 26.16 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.058 / Rrim(I) all: 0.155 / Net I/σ(I): 11.2 / Num. measured all: 99947 / Scaling rejects: 81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.21-2.286.80.854809411970.7750.3520.9263.495.5
9.12-44.456.50.09615022320.9920.040.1052199.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
Aimlessdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VLI

6vli


Resolution: 2.211→44.447 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2829 1421 9.94 %
Rwork0.2274 12875 -
obs0.233 14296 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.34 Å2 / Biso mean: 43.2087 Å2 / Biso min: 6.02 Å2
Refinement stepCycle: final / Resolution: 2.211→44.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 6 143 2340
Biso mean--64.02 36.79 -
Num. residues----285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042235
X-RAY DIFFRACTIONf_angle_d0.6533033
X-RAY DIFFRACTIONf_chiral_restr0.034349
X-RAY DIFFRACTIONf_plane_restr0.005397
X-RAY DIFFRACTIONf_dihedral_angle_d15.6041379
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2111-2.29020.32431390.2656125695
2.2902-2.38190.35791380.262124997
2.3819-2.49030.31971370.239127797
2.4903-2.62150.26861480.2331124997
2.6215-2.78580.29391400.2411128497
2.7858-3.00080.2691350.2451131298
3.0008-3.30270.28681390.2332128298
3.3027-3.78040.26421530.205130398
3.7804-4.7620.24421460.1885130598
4.762-44.4470.30771460.2455135898
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)
14.2111-2.5533-0.04278.0593-2.45274.4293-0.1241-0.40710.30850.19750.2968-0.1312-0.5077-0.008-0.10910.2771-0.03270.04060.163-0.05790.190734.291433.56685.8865
23.2389-0.9596-0.46291.125-1.1111.5392-0.2315-0.14460.0150.08060.1199-0.08870.13290.08660.04630.2515-0.00110.06150.1143-0.03850.172541.30522.81635.4115
33.30670.42140.14592.9491-0.41852.1105-0.05850.0703-0.7984-0.21850.65190.30210.5701-0.122-0.07470.39630.0620.09810.3240.15180.329718.980816.79947.4854
40.7642-2.0684-0.7588.84223.94954.46220.3819-0.8029-1.14330.4739-0.92441.29690.287-0.29110.11580.3269-0.0262-0.07190.26660.11180.60462.26418.40675.7544
51.732-1.0539-1.15834.20390.02090.97120.31190.27240.0386-0.5326-0.24870.3977-0.2711-0.1530.13381.45681.1094-0.48560.5245-1.05061.2503-0.91437.544713.5715
63.42761.2641.35925.6766-0.75075.16050.0169-0.6979-1.01210.2651-0.1790.26450.3685-0.51940.00050.1399-0.0217-0.02660.26930.04070.3719.881518.01188.2228
77.34961.99962.66783.18283.16053.28160.1792-0.9098-1.00171.286-0.1953-0.03021.3019-0.5104-0.09730.5161-0.00290.13020.24830.02410.331328.573110.79144.9124
83.25430.0973-1.88082.96630.25674.2838-0.0140.1387-0.1538-0.19780.1294-0.20860.14860.0969-0.1010.2513-0.00380.02180.1355-0.02910.145630.709524.0216-13.1909
93.1844-1.833-0.63161.0012-0.19111.58480.34870.27850.26-0.301-0.1710.083-0.2203-0.1391-0.13290.23920.02220.020.1596-0.0060.293214.804925.9576-0.4584
104.79940.58330.81446.121.90436.08810.21770.8477-0.5844-0.6755-0.0903-0.29550.2898-0.2511-0.15280.2922-0.00650.03290.3823-0.08890.312212.290619.6898-2.7086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 42 )A23 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 96 )A43 - 96
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 111 )A97 - 111
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 131 )A112 - 131
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 137 )A132 - 137
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 165 )A138 - 165
7X-RAY DIFFRACTION7chain 'B' and (resid 22 through 30 )B22 - 30
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 83 )B31 - 83
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 130 )B84 - 130
10X-RAY DIFFRACTION10chain 'B' and (resid 131 through 163 )B131 - 163

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