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- PDB-6n8b: Crystal structure of transcription regulator AcaB from uropathoge... -

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Basic information

Entry
Database: PDB / ID: 6n8b
TitleCrystal structure of transcription regulator AcaB from uropathogenic E. coli
Componentstranscription regulator AcaB
KeywordsTRANSCRIPTION / uropathogenic E. coli / New-Delhi metallo-beta-lactamase / NDM / A/C plasmid / AcaB / transcription regulation
Function / homologyDUF1845 domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.94 Å
AuthorsLuo, Z. / Hancock, S.J. / Schembri, M.A. / Kobe, B.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1106590 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1033799 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1067455 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1071659 Australia
CitationJournal: Nat Microbiol / Year: 2020
Title: Comprehensive analysis of IncC plasmid conjugation identifies a crucial role for the transcriptional regulator AcaB.
Authors: Hancock, S.J. / Phan, M.D. / Luo, Z. / Lo, A.W. / Peters, K.M. / Nhu, N.T.K. / Forde, B.M. / Whitfield, J. / Yang, J. / Strugnell, R.A. / Paterson, D.L. / Walsh, T.R. / Kobe, B. / Beatson, S.A. / Schembri, M.A.
History
DepositionNov 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: transcription regulator AcaB
B: transcription regulator AcaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9483
Polymers47,9082
Non-polymers401
Water18010
1
A: transcription regulator AcaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9942
Polymers23,9541
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: transcription regulator AcaB


Theoretical massNumber of molelcules
Total (without water)23,9541
Polymers23,9541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.188, 167.188, 167.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLNGLN(chain A and (resseq 19:22 or (resid 23 and (name...AA19 - 3519 - 35
12VALVALLEULEU(chain A and (resseq 19:22 or (resid 23 and (name...AA37 - 5637 - 56
13ILEILEVALVAL(chain A and (resseq 19:22 or (resid 23 and (name...AA58 - 6858 - 68
14THRTHRASPASP(chain A and (resseq 19:22 or (resid 23 and (name...AA70 - 10070 - 100
15METMETILEILE(chain A and (resseq 19:22 or (resid 23 and (name...AA102 - 127102 - 127
16LYSLYSALAALA(chain A and (resseq 19:22 or (resid 23 and (name...AA129 - 166129 - 166
17ILEILELYSLYS(chain A and (resseq 19:22 or (resid 23 and (name...AA169 - 211169 - 211
21SERSERGLNGLN(chain B and (resseq 19:22 or (resid 23 and (name...BB19 - 3519 - 35
22VALVALLEULEU(chain B and (resseq 19:22 or (resid 23 and (name...BB37 - 5637 - 56
23ILEILEVALVAL(chain B and (resseq 19:22 or (resid 23 and (name...BB58 - 6858 - 68
24THRTHRASPASP(chain B and (resseq 19:22 or (resid 23 and (name...BB70 - 10070 - 100
25METMETILEILE(chain B and (resseq 19:22 or (resid 23 and (name...BB102 - 127102 - 127
26LYSLYSALAALA(chain B and (resseq 19:22 or (resid 23 and (name...BB129 - 166129 - 166
27ILEILELYSLYS(chain B and (resseq 19:22 or (resid 23 and (name...BB169 - 211169 - 211

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Components

#1: Protein transcription regulator AcaB


Mass: 23954.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C4NVV6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 4.06 Å3/Da / Density % sol: 69.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris, pH 8.0, 23% (w/v) PEG 350 monomethyl ether, in the presence of alpha-chymotrypsin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.94→44.68 Å / Num. obs: 16642 / % possible obs: 100 % / Redundancy: 22.2 % / Biso Wilson estimate: 57.2293254425 Å2 / Net I/σ(I): 19.33
Reflection shellResolution: 2.94→3.05 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.94→44.68 Å / SU ML: 0.354139512882 / Cross valid method: FREE R-VALUE / σ(F): 1.34606795746 / Phase error: 25.1849787301
RfactorNum. reflection% reflection
Rfree0.257851722805 917 5.52343091194 %
Rwork0.227957000307 --
obs0.229569350883 16602 99.5323741007 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.992440657 Å2
Refinement stepCycle: LAST / Resolution: 2.94→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 1 10 3073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004987778626953098
X-RAY DIFFRACTIONf_angle_d0.8844132696624178
X-RAY DIFFRACTIONf_chiral_restr0.0514417647727488
X-RAY DIFFRACTIONf_plane_restr0.00468815481027542
X-RAY DIFFRACTIONf_dihedral_angle_d17.9762828591934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9408-3.09580.3383275234321450.3113316751032129X-RAY DIFFRACTION96.7247979583
3.0958-3.28970.2946333914131070.3013931622392251X-RAY DIFFRACTION100
3.2897-3.54370.2851946126721570.2681886866672211X-RAY DIFFRACTION100
3.5437-3.90010.2800016910691430.2369587464882222X-RAY DIFFRACTION100
3.9001-4.4640.2421578330031280.2008333445452241X-RAY DIFFRACTION100
4.464-5.62240.2157837281021100.2105553255582286X-RAY DIFFRACTION100
5.6224-44.6880.2303251411741270.1918206948022345X-RAY DIFFRACTION99.9595632835
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)
18.097436124512.90644673952-0.2288416846362.63048476149-0.5078383203772.28969595376-0.0451144474699-0.522360598322-0.3321499674540.0358296812682-0.321854591695-0.2327880795080.1192825314350.372038192890.2855584937110.2536474124750.03945679541470.07213854950820.3429253538860.07568203914570.347652876957-20.6046262229.8550641424-8.8340321865
28.562859871933.96816531775-0.9390996486214.9089348405-0.6036074640341.220753207080.1132241614-0.109885946527-0.2607374682970.11251073727-0.1648934646050.1488072127220.229273525399-0.08492795920440.06364605061690.276930244697-0.01708750054410.01284081604570.2973741123960.01911834212320.289034887856-30.2173948228.0346550616-10.8774158505
35.056442970.2995566960450.06628863761762.27456347254-0.409812459536.30771762110.0967619367814-1.02964742351.007994623480.0875410926211-0.2516012516660.474917609774-0.615280420628-0.1916999173030.05661307143070.384509431099-0.03915981636380.07128135052810.475877406457-0.1646932819330.588258919105-18.929636228946.7974623723-6.08808268035
44.23256211833-2.892555182131.549660084333.68147901362-0.09636453711722.59441734925-0.345764495441-0.1598376758460.3006625893160.3229531833150.5099254108720.480227861635-0.64426660271-0.430816028141-0.1422812580430.4183509826040.07401027043780.07492504341850.4239520371690.06963499615460.462133245317-28.536662016419.065551427424.9114394317
54.1368415132-1.707588542991.320748723894.59003275741-0.1759079276774.313909353590.29287581870.4530765323740.42377562182-1.4532154991-0.0174077654275-0.2159154206750.196549835814-0.119801749833-0.275012512220.3440528844610.09821991716840.01912254552030.5454362580010.02225128914730.340317157664-21.4305799611.928593694611.0870449748
63.87889842845-2.34016426820.5522853374697.90996092795-1.224600604833.426348674910.04749223959620.025184829448-0.0410579960399-0.1813697374510.06426093821440.0558766392456-0.02923433762250.00359887586113-0.07999147711730.235523880674-0.0004727326992760.001759654563320.275998174870.00378769209490.141122143278-20.06450816628.3587825244722.5187774553
74.78614645413-2.641277602932.554488147876.91688258158-3.795620480796.62277512722-0.526708491425-0.4559694175340.9959275912980.5886052005090.483621495792-0.143723359011-0.736911452256-0.005267205402060.08204569989480.603377243496-0.1138838962390.05043192632070.3404601797050.01202620515540.596334833711-19.300130550930.408684507326.2527882222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 182 )
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 212 )
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 61 )
5X-RAY DIFFRACTION5chain 'B' and (resid 62 through 96 )
6X-RAY DIFFRACTION6chain 'B' and (resid 97 through 182 )
7X-RAY DIFFRACTION7chain 'B' and (resid 183 through 212 )

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