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- PDB-6t3h: Structure of the Rap conjugation gene regulator of the plasmid pL... -

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Basic information

Entry
Database: PDB / ID: 6t3h
TitleStructure of the Rap conjugation gene regulator of the plasmid pLS20 in apo form
ComponentsResponse regulator aspartate phosphatase
KeywordsTRANSCRIPTION / Response regulator / conjugation
Function / homologyTetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Response regulator aspartate phosphatase
Function and homology information
Biological speciesBacillus subtilis subsp. natto (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.039 Å
AuthorsCrespo, I. / Bernardo, N. / Meijer, W.J.J. / Boer, D.R.
Funding support Spain, 3items
OrganizationGrant numberCountry
Ministry of Economy and CompetitivenessBIO2016-77883-C2-2-P Spain
Ministry of Economy and CompetitivenessBIO2016-77883-C2-2-P Spain
Ministry of Economy and CompetitivenessFIS2015-72574-EXP Spain
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Inactivation of the dimeric RappLS20 anti-repressor of the conjugation operon is mediated by peptide-induced tetramerization.
Authors: Crespo, I. / Bernardo, N. / Miguel-Arribas, A. / Singh, P.K. / Luque-Ortega, J.R. / Alfonso, C. / Malfois, M. / Meijer, W.J.J. / Boer, D.R.
History
DepositionOct 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _software.name
Revision 1.2Aug 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator aspartate phosphatase
B: Response regulator aspartate phosphatase


Theoretical massNumber of molelcules
Total (without water)89,0032
Polymers89,0032
Non-polymers00
Water0
1
A: Response regulator aspartate phosphatase
B: Response regulator aspartate phosphatase

A: Response regulator aspartate phosphatase
B: Response regulator aspartate phosphatase


Theoretical massNumber of molelcules
Total (without water)178,0064
Polymers178,0064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area11400 Å2
ΔGint-69 kcal/mol
Surface area66910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.790, 174.487, 49.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 9 through 364)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 9 - 364 / Label seq-ID: 9 - 364

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 9 through 364)AA
2chain BBB

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Components

#1: Protein Response regulator aspartate phosphatase


Mass: 44501.383 Da / Num. of mol.: 2 / Mutation: C-terminal His-tag
Source method: isolated from a genetically manipulated source
Details: plasmid pLS20
Source: (gene. exp.) Bacillus subtilis subsp. natto (bacteria)
Gene: rapA / Plasmid: pET-28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9RIY6

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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: 2.66 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% Peg 6000, 0.1M Hepes pH 7. Protein concentration 10mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97927 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2016 / Details: KB mirrors
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 3.039→87.2 Å / Num. obs: 18645 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 94.17 Å2 / CC1/2: 0.607 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.044 / Rrim(I) all: 0.075 / Net I/σ(I): 14.8
Reflection shellResolution: 3.039→3.092 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 797 / CC1/2: 0.607 / Rpim(I) all: 0.615 / Rrim(I) all: 1.041 / % possible all: 82.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSJun 1, 2017data reduction
autoPROCstaraniso 1.0.4data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ulq

3ulq


Resolution: 3.039→53.231 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.62
RfactorNum. reflection% reflection
Rfree0.2593 925 4.96 %
Rwork0.2013 --
obs0.2042 18639 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 284.67 Å2 / Biso mean: 95.4016 Å2 / Biso min: 27.85 Å2
Refinement stepCycle: final / Resolution: 3.039→53.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5961 0 0 0 5961
Num. residues----713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046115
X-RAY DIFFRACTIONf_angle_d0.7348250
X-RAY DIFFRACTIONf_chiral_restr0.041855
X-RAY DIFFRACTIONf_plane_restr0.0051050
X-RAY DIFFRACTIONf_dihedral_angle_d9.3273626
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3256X-RAY DIFFRACTION14.843TORSIONAL
12B3256X-RAY DIFFRACTION14.843TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0393-3.19960.44561100.3237239691
3.1996-3.40.34091420.2582592100
3.4-3.66250.28181190.22229488
3.6625-4.03090.24021150.2038242292
4.0309-4.61390.2581600.1677259299
4.6139-5.81190.26121340.1978265198
5.8119-53.2310.22341450.1893276798
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)
10.18250.29040.1270.61960.62741.3936-0.1237-0.40490.03850.7273-0.04261.45990.0568-0.2075-0.06480.4088-0.02730.31350.43210.04421.0178-26.14799.0851-5.1236
22.2593-0.0526-0.46521.3407-1.78782.53060.07410.4284-0.1447-0.2874-0.17270.07520.16850.1986-0.00120.58730.0452-0.06790.3646-0.09890.341-12.125727.129-26.0923
31.0459-1.30430.57431.9526-0.15831.5477-0.1368-0.35660.52420.0696-0.0471-0.1246-0.1189-0.6542-0.00010.41320.0484-0.0160.63560.02630.582-21.545150.4285-20.1781
40.2548-0.2593-0.0950.2679-0.08160.62480.05770.16160.2002-0.5584-0.0792-0.24730.12380.17240.00020.6872-0.0370.21050.4837-0.00970.898525.518912.7117-14.5841
52.0411-0.1598-0.31493.72191.15190.9049-0.169-0.4972-0.30080.09350.19340.1069-0.15620.103900.56060.0083-0.05230.57680.07250.35956.359131.99421.892
60.83460.5202-0.17331.2375-0.55742.2173-0.18150.2410.8346-0.1152-0.1620.1206-0.07390.8634-0.0010.5223-0.0248-0.11960.66170.01940.68489.52256.0111-7.0294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 9:114)A9 - 114
2X-RAY DIFFRACTION2(chain A and resseq 115:249)A115 - 249
3X-RAY DIFFRACTION3(chain A and resseq 250:365)A250 - 365
4X-RAY DIFFRACTION4(chain B and resseq 9:100)B9 - 100
5X-RAY DIFFRACTION5(chain B and resseq 101:247)B101 - 247
6X-RAY DIFFRACTION6(chain B and resseq 248:364)B248 - 364

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