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- PDB-6t46: Structure of the Rap conjugation gene regulator of the plasmid pL... -

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Basic information

Entry
Database: PDB / ID: 6t46
TitleStructure of the Rap conjugation gene regulator of the plasmid pLS20 in complex with the Phr* peptide
Components
  • Quorum-sensing secretion protein (processed)
  • Response regulator aspartate phosphatase
KeywordsTRANSCRIPTION / Response regulator / conjugation
Function / homologyTetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Response regulator aspartate phosphatase / Uncharacterized protein
Function and homology information
Biological speciesBacillus subtilis subsp. natto (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsCrespo, I. / Bernardo, N. / Meijer, W.J.J. / Boer, D.R.
Funding support Spain, 2items
OrganizationGrant numberCountry
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 12, 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

Downloads & links

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Assembly

Deposited unit
A: Response regulator aspartate phosphatase
B: Quorum-sensing secretion protein (processed)
C: Response regulator aspartate phosphatase
D: Quorum-sensing secretion protein (processed)
E: Response regulator aspartate phosphatase
F: Quorum-sensing secretion protein (processed)
G: Response regulator aspartate phosphatase
H: Quorum-sensing secretion protein (processed)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,70812
Polymers196,5798
Non-polymers1294
Water34219
1
A: Response regulator aspartate phosphatase
B: Quorum-sensing secretion protein (processed)
C: Response regulator aspartate phosphatase
D: Quorum-sensing secretion protein (processed)
hetero molecules

A: Response regulator aspartate phosphatase
B: Quorum-sensing secretion protein (processed)
C: Response regulator aspartate phosphatase
D: Quorum-sensing secretion protein (processed)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,76714
Polymers196,5798
Non-polymers1886
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area17800 Å2
ΔGint-150 kcal/mol
Surface area62430 Å2
MethodPISA
2
E: Response regulator aspartate phosphatase
F: Quorum-sensing secretion protein (processed)
G: Response regulator aspartate phosphatase
H: Quorum-sensing secretion protein (processed)
hetero molecules

E: Response regulator aspartate phosphatase
F: Quorum-sensing secretion protein (processed)
G: Response regulator aspartate phosphatase
H: Quorum-sensing secretion protein (processed)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,65010
Polymers196,5798
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area16140 Å2
ΔGint-112 kcal/mol
Surface area63960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.670, 93.282, 167.687
Angle α, β, γ (deg.)90.000, 94.970, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain C and resid 9 through 367)
31(chain E and resid 9 through 367)
41(chain G and resid 9 through 367)
12chain B
22chain D
32chain F
42chain H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUchain AAA9 - 3679 - 367
21PROPROLEULEU(chain C and resid 9 through 367)CC9 - 3679 - 367
31PROPROLEULEU(chain E and resid 9 through 367)EE9 - 3679 - 367
41PROPROLEULEU(chain G and resid 9 through 367)GG9 - 3679 - 367
12GLNGLNTYRTYRchain BBB1 - 540 - 44
22GLNGLNTYRTYRchain DDD1 - 540 - 44
32GLNGLNTYRTYRchain FFF1 - 540 - 44
42GLNGLNTYRTYRchain HHH1 - 540 - 44

NCS ensembles :
ID
1
2

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Components

#1: Protein
Response regulator aspartate phosphatase


Mass: 44501.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: plasmid pLS20
Source: (gene. exp.) Bacillus subtilis subsp. natto (bacteria)
Gene: rapA / Details (production host): p-ET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9RIY6
#2: Protein/peptide
Quorum-sensing secretion protein (processed)


Mass: 4643.364 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis subsp. natto (bacteria) / References: UniProt: E9RIY7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 6.8
Details: 2.5% PEG8K, 8% Etilenglicol, 0.1M MES pH6.8, Rap 10mg/mL, 1:5 RAP:Phr (QKGMY)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.12712 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2016 / Details: KB mirrors, Si coated
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12712 Å / Relative weight: 1
ReflectionResolution: 2.45→45.424 Å / Num. obs: 44873 / % possible obs: 95.9 % / Redundancy: 2.2 % / Biso Wilson estimate: 92.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.037 / Rrim(I) all: 0.053 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.45-2.4923.20.7881.3940.6220.7591.0742.8
6.643-45.4242.10.01869500.9930.0160.02396.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
autoPROC1.0.5data scaling
PDB_EXTRACT3.25data extraction
XDSJun 1, 2017data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T3H

6t3h


Resolution: 2.45→45.424 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.49
RfactorNum. reflection% reflection
Rfree0.2621 2338 5.21 %
Rwork0.202 --
obs0.2051 44849 67.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 204.8 Å2 / Biso mean: 68.561 Å2 / Biso min: 19.9 Å2
Refinement stepCycle: final / Resolution: 2.45→45.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12251 0 4 19 12274
Biso mean--62.24 60.51 -
Num. residues----1468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112560
X-RAY DIFFRACTIONf_angle_d1.61216935
X-RAY DIFFRACTIONf_chiral_restr0.0811753
X-RAY DIFFRACTIONf_plane_restr0.012157
X-RAY DIFFRACTIONf_dihedral_angle_d12.8517452
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6955X-RAY DIFFRACTION22.21TORSIONAL
12C6955X-RAY DIFFRACTION22.21TORSIONAL
13E6955X-RAY DIFFRACTION22.21TORSIONAL
14G6955X-RAY DIFFRACTION22.21TORSIONAL
21B97X-RAY DIFFRACTION22.21TORSIONAL
22D97X-RAY DIFFRACTION22.21TORSIONAL
23F97X-RAY DIFFRACTION22.21TORSIONAL
24H97X-RAY DIFFRACTION22.21TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.49990.507100.381314
2.4999-2.55430.3685160.346238010
2.5543-2.61370.4082390.34468919
2.6137-2.6790.4441700.3362110430
2.679-2.75150.4194900.3197155542
2.7515-2.83240.3921030.314191953
2.8324-2.92380.37281110.3188233763
2.9238-3.02830.35851560.3045284677
3.0283-3.14950.34681890.294332191
3.1495-3.29280.3591870.2811353996
3.2928-3.46640.3272090.2458352397
3.4664-3.68340.29581950.2362316186
3.6834-3.96770.2911970.2056353796
3.9677-4.36670.24141790.1603362097
4.3667-4.99790.20572010.1486358497
4.9979-6.29410.23651930.1889362297
6.2941-45.4240.18981930.1598364396
Refinement TLS params.Method: refined / Origin x: 92.281 Å / Origin y: 9.3905 Å / Origin z: -41.49 Å
111213212223313233
T0.2166 Å20.0042 Å20.0055 Å2-0.2834 Å20.0186 Å2--0.2518 Å2
L0.0809 °20.039 °20.0531 °2-0.2572 °20.159 °2--0.3362 °2
S0.0463 Å °-0.1269 Å °-0.0612 Å °-0.0066 Å °-0.048 Å °0.0248 Å °-0.0048 Å °0.0236 Å °-0.0003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 367
2X-RAY DIFFRACTION1allB1 - 5
3X-RAY DIFFRACTION1allC6 - 368
4X-RAY DIFFRACTION1allD1 - 5
5X-RAY DIFFRACTION1allE8 - 368
6X-RAY DIFFRACTION1allF1 - 5
7X-RAY DIFFRACTION1allG7 - 371
8X-RAY DIFFRACTION1allH1 - 5
9X-RAY DIFFRACTION1allI2 - 20
10X-RAY DIFFRACTION1allJ1 - 2
11X-RAY DIFFRACTION1allJ3
12X-RAY DIFFRACTION1allK1

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