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- PDB-6gyg: X-ray structure of the apo form of the establishement gene regula... -

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Basic information

Entry
Database: PDB / ID: 6gyg
TitleX-ray structure of the apo form of the establishement gene regulator Reg576 of the G+ plasmid p576
ComponentsTranscription regulator Reg576
KeywordsTRANSCRIPTION / Plasmid establishment DNA bindig protein Gene repressor Gram-positive bacteria Bacterial conjugation
Function / homology:
Function and homology information
Biological speciesBacillus altitudinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsCrespo, I. / Meijer, W.J.J. / Boer, D.R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-77883-C2-2-P Spain
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Novel regulatory mechanism of establishment genes of conjugative plasmids.
Authors: Val-Calvo, J. / Luque-Ortega, J.R. / Crespo, I. / Miguel-Arribas, A. / Abia, D. / Sanchez-Hevia, D.L. / Serrano, E. / Gago-Cordoba, C. / Ares, S. / Alfonso, C. / Rojo, F. / Wu, L.J. / Boer, D.R. / Meijer, W.J.J.
History
DepositionJun 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 10, 2019Group: Data collection / Structure summary / Category: audit_author
Revision 1.4Oct 16, 2019Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5May 1, 2024Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription regulator Reg576
B: Transcription regulator Reg576


Theoretical massNumber of molelcules
Total (without water)17,4842
Polymers17,4842
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-39 kcal/mol
Surface area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.278, 44.278, 141.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Transcription regulator Reg576


Mass: 8742.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: plasmid p576 / Source: (gene. exp.) Bacillus altitudinis (bacteria) / Gene: ABW03_19300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J1KER7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.98 Å3/Da / Density % sol: 37.84 % / Description: Needles
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: Protein was concentrated to 25 mg/mL in [20 mM Tris (pH8.0), 250 mM NaCl]. Crystals of Reg576 were obtained in 130 mM potassium bromide, 25% PEG 2000 monomethylether by the sitting-drop ...Details: Protein was concentrated to 25 mg/mL in [20 mM Tris (pH8.0), 250 mM NaCl]. Crystals of Reg576 were obtained in 130 mM potassium bromide, 25% PEG 2000 monomethylether by the sitting-drop vapor-diffusion method at 18 deg. C, in drops of 1 uL + 1 uL (protein:reservoir). Needle-shaped crystals appeared in less t han a week. Cryo-cooling in liquid nitrogen was carried out using a cryo-protecting solution containing reservoir solution supplemented with 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford cryostream 600 series
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2017 / Details: KB mirrors
RadiationMonochromator: Channel cut Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.979→42.25 Å / Num. obs: 8828 / % possible obs: 92.6 % / Redundancy: 11.6 % / Biso Wilson estimate: 47.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Net I/σ(I): 12.5
Reflection shellResolution: 1.979→2.013 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.959 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 55 / CC1/2: 0.502 / % possible all: 41.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
autoPROCsnapshot_20170508data scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: fragments

Resolution: 1.98→42.25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.884 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25596 453 5.1 %RANDOM
Rwork0.20708 ---
obs0.20981 8373 84.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-0 Å2-0 Å2
2--0.32 Å2-0 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.98→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 0 33 1083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0141065
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171047
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.6661418
X-RAY DIFFRACTIONr_angle_other_deg1.0581.6392459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7415118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45423.7162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.615241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.215156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02191
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_it3.0253.984478
X-RAY DIFFRACTIONr_mcbond_other3.0283.972477
X-RAY DIFFRACTIONr_mcangle_it4.2665.933594
X-RAY DIFFRACTIONr_mcangle_other4.2635.947595
X-RAY DIFFRACTIONr_scbond_it4.424.769587
X-RAY DIFFRACTIONr_scbond_other4.4044.75585
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0226.856824
X-RAY DIFFRACTIONr_long_range_B_refined8.62745.0941192
X-RAY DIFFRACTIONr_long_range_B_other8.61245.091191
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.979→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 3 -
Rwork0.331 108 -
obs--14.55 %
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)
19.8380.6247-1.79690.464-0.60020.90.03290.20250.33250.09750.0065-0.0224-0.1442-0.0214-0.03940.0871-0.020.01450.0136-0.01750.11890.492131.73242.1545
20.8094-1.037-0.72362.87262.17991.67760.0034-0.35010.16170.01380.175-0.12160.00230.1893-0.17840.0785-0.09840.04250.2855-0.13890.1104-2.178923.933713.3807
32.19061.74981.28383.87733.33892.9164-0.1821-0.23620.07070.08250.10070.12540.11050.13650.08140.06960.00720.00820.1094-0.03170.0884-4.066613.90212.3969
47.09413.93160.08552.28050.18291.68930.07850.1575-0.16720.0866-0.0009-0.11530.28590.1245-0.07760.07990.00550.02970.11050.01180.09195.071510.9732-8.0262
57.4686-5.33622.29919.2793-1.09811.3879-0.33940.13540.1150.65070.01910.2292-0.03480.10.32030.0478-0.00050.03280.05580.00060.13692.182233.09124.488
62.56051.22742.70171.51511.07296.07860.00020.01730.0156-0.25370.0583-0.1834-0.2516-0.0151-0.05850.11-0.00130.04010.0394-0.02020.10523.845718.8912-3.0303
73.68642.6837-3.1753.5865-2.06593.0584-0.15550.17490.0891-0.21240.1174-0.04380.1515-0.28820.03810.067-0.02090.01390.0831-0.03790.1008-7.444921.91770.9665
80.8410.4298-1.16518.07160.45063.03330.10160.0760.10030.10130.0980.1424-0.1964-0.2271-0.19960.04310.00360.02060.065-0.02580.0648-13.393127.231116.4155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 18
2X-RAY DIFFRACTION2A19 - 33
3X-RAY DIFFRACTION3A34 - 49
4X-RAY DIFFRACTION4A50 - 65
5X-RAY DIFFRACTION5B6 - 12
6X-RAY DIFFRACTION6B13 - 27
7X-RAY DIFFRACTION7B28 - 46
8X-RAY DIFFRACTION8B47 - 66

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