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

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Basic information

Entry
Database: PDB / ID: 6vmh
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 / Regulatory protein CII
Function and homology information
Biological speciesEscherichia phage 186 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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
DepositionJan 27, 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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Regulatory protein CII
C: Regulatory protein CII


Theoretical massNumber of molelcules
Total (without water)34,9702
Polymers34,9702
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-32 kcal/mol
Surface area8840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.860, 59.860, 112.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Regulatory protein CII


Mass: 17484.885 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion
Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.75→29.93 Å / Num. obs: 6506 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.948 / Rmerge(I) obs: 0.48 / Rpim(I) all: 0.141 / Rrim(I) all: 0.501 / Net I/σ(I): 4.9 / Num. measured all: 80395 / Scaling rejects: 41
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
2.75-2.912.81.312119889390.7530.3761.3662.5100
8.7-29.939.70.22822822360.9160.0770.2427.797.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
iMOSFLMdata reduction
Aimless0.5.25data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VLI

6vli


Resolution: 2.75→29.93 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0.46 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 1092 16.85 %
Rwork0.2122 5389 -
obs0.2209 6481 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110 Å2 / Biso mean: 33.5902 Å2 / Biso min: 13.33 Å2
Refinement stepCycle: final / Resolution: 2.75→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 64 1402
Biso mean---26.69 -
Num. residues----167
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.75-2.880.30021540.2761636790
2.88-3.030.32671160.2616667783
3.03-3.220.32561400.2344655795
3.22-3.460.28791350.2354671806
3.46-3.810.28981170.2004677794
3.81-4.360.21621320.1798679811
4.36-5.490.23341350.179694829
5.49-29.930.22581630.2059710873
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)
16.8005-2.0134-0.50611.9171.20795.6681-0.10550.08951.38570.0420.1567-1.2712-1.3920.90630.28660.6297-0.0193-0.10620.4787-0.02390.751311.192538.880518.9171
22.0811-0.2428-1.36781.7238-0.09621.7202-0.06860.6986-0.0778-0.26950.15370.3528-0.1597-0.4426-0.02230.0666-0.0001-0.01440.2688-0.0310.2181-0.335925.25116.0489
31.68070.9656-0.66372.18381.01032.5728-0.1260.061-0.01960.02620.3071-0.32450.22050.40120.0420.09970.00140.07460.388-0.06380.18812.402523.345412.0538
44.4170.0285-1.56113.55950.20861.86530.25490.0739-0.8894-0.54690.205-0.84920.70410.60760.10390.5344-0.0558-0.02690.74390.1091.335913.577712.037517.1555
53.87-1.56612.67084.74712.28754.5906-0.038-1.2574-0.28160.62560.267-0.1060.3880.0579-0.11420.1084-0.0526-0.06350.54490.10810.284810.214719.174330.3723
63.27710.6506-0.39914.69541.04772.6480.3773-0.47560.17670.6988-0.13590.35830.04840.1403-0.10150.2124-0.0833-0.02240.37660.01870.25130.221124.792131.5017
70.5112-0.2542-0.1811.0213-0.28290.217-0.0738-0.3430.41990.1913-0.1368-0.1729-0.16230.20590.0467-0.0363-0.0308-0.1280.41530.00590.1936.265331.924724.5893
85.0731-0.4874-0.1361.0111.13463.4566-0.2101-0.28750.2756-0.063-0.09990.2848-0.11280.0994-0.25920.0407-0.0720.00670.46590.09240.395113.521423.836922.9975
98.51040.1244-0.6164.89161.7527.9136-0.16630.17550.8574-0.32150.28990.0126-0.59720.0931-0.01780.0705-0.0591-0.01680.3466-0.15830.496820.350529.851717.9911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 23 through 30 )B23 - 30
2X-RAY DIFFRACTION2chain 'B' and (resid 31 through 72 )B31 - 72
3X-RAY DIFFRACTION3chain 'B' and (resid 73 through 106 )B73 - 106
4X-RAY DIFFRACTION4chain 'C' and (resid 24 through 30 )C24 - 30
5X-RAY DIFFRACTION5chain 'C' and (resid 31 through 42 )C31 - 42
6X-RAY DIFFRACTION6chain 'C' and (resid 43 through 72 )C43 - 72
7X-RAY DIFFRACTION7chain 'C' and (resid 73 through 83 )C73 - 83
8X-RAY DIFFRACTION8chain 'C' and (resid 84 through 96 )C84 - 96
9X-RAY DIFFRACTION9chain 'C' and (resid 97 through 106 )C97 - 106

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