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- PDB-6n8a: Crystal structure of selenomethionine-containing AcaB from uropat... -

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Basic information

Entry
Database: PDB / ID: 6n8a
TitleCrystal structure of selenomethionine-containing 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 / homologyPlasmid-related protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4011 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 28, 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

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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)44,2043
Polymers44,1692
Non-polymers351
Water1086
1
A: transcription regulator AcaB


Theoretical massNumber of molelcules
Total (without water)22,0841
Polymers22,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: transcription regulator AcaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1202
Polymers22,0841
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)169.168, 169.168, 169.168
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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 19:35 or resseq 37:55 or (resid...A19 - 35
121(chain A and (resseq 19:35 or resseq 37:55 or (resid...A37
131(chain A and (resseq 19:35 or resseq 37:55 or (resid...A39 - 56
141(chain A and (resseq 19:35 or resseq 37:55 or (resid...A58 - 66
151(chain A and (resseq 19:35 or resseq 37:55 or (resid...A68 - 93
161(chain A and (resseq 19:35 or resseq 37:55 or (resid...A95 - 100
171(chain A and (resseq 19:35 or resseq 37:55 or (resid...A103 - 127
181(chain A and (resseq 19:35 or resseq 37:55 or (resid...A129 - 133
191(chain A and (resseq 19:35 or resseq 37:55 or (resid...A135 - 166
1101(chain A and (resseq 19:35 or resseq 37:55 or (resid...A169 - 185
1111(chain A and (resseq 19:35 or resseq 37:55 or (resid...A187 - 208
211(chain B and (resseq 19:35 or resseq 37:55 or (resid...B19 - 35
221(chain B and (resseq 19:35 or resseq 37:55 or (resid...B37
231(chain B and (resseq 19:35 or resseq 37:55 or (resid...B39 - 56
241(chain B and (resseq 19:35 or resseq 37:55 or (resid...B58 - 66
251(chain B and (resseq 19:35 or resseq 37:55 or (resid...B68 - 93
261(chain B and (resseq 19:35 or resseq 37:55 or (resid...B95 - 100
271(chain B and (resseq 19:35 or resseq 37:55 or (resid...B103 - 127
281(chain B and (resseq 19:35 or resseq 37:55 or (resid...B129 - 133
291(chain B and (resseq 19:35 or resseq 37:55 or (resid...B135 - 166
2101(chain B and (resseq 19:35 or resseq 37:55 or (resid...B169 - 185
2111(chain B and (resseq 19:35 or resseq 37:55 or (resid...B187 - 208

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Components

#1: Protein transcription regulator AcaB


Mass: 22084.293 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.57 Å3/Da / Density % sol: 73.11 %
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: 3.4→48.83 Å / Num. obs: 11255 / % possible obs: 100 % / Redundancy: 35.1 % / Biso Wilson estimate: 83.5189339063 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.02 / Rrim(I) all: 0.117 / Net I/σ(I): 31.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.4-3.6736.90.3523100.9910.0580.355100
9-48.8332.20.0656450.9990.0110.06699.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
AutoSolphasing
XDSdata reduction
RefinementResolution: 3.4011→48.83 Å / SU ML: 0.507892100266 / Cross valid method: FREE R-VALUE / σ(F): 1.37264257339 / Phase error: 25.0569534687
RfactorNum. reflection% reflection
Rfree0.249288991736 593 5.26923760441 %
Rwork0.222882474186 --
obs0.224431912849 11254 99.99111506 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 76.2353599657 Å2
Refinement stepCycle: LAST / Resolution: 3.4011→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3057 0 1 6 3064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002152389769893093
X-RAY DIFFRACTIONf_angle_d0.501091811144171
X-RAY DIFFRACTIONf_chiral_restr0.0372758401069487
X-RAY DIFFRACTIONf_plane_restr0.00219318713889541
X-RAY DIFFRACTIONf_dihedral_angle_d16.54700497371931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4011-3.74320.3006145794161310.2776309696762651X-RAY DIFFRACTION100
3.7432-4.28460.2927349946121540.2345404979812634X-RAY DIFFRACTION100
4.2846-5.39710.229234864171580.218226284922645X-RAY DIFFRACTION100
5.3971-48.83960.2223605076041500.1987544908942731X-RAY DIFFRACTION99.9653018737
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)
12.43359517076-2.157534872640.2961593538612.08793138565-0.2478345429480.02543593352640.173450743118-0.0365474719577-0.2889668664670.208301589465-0.4292390603310.263138156955-0.07296195620080.2425843082550.2325184045490.702731349988-0.1734353574270.1346331644220.760120320129-0.1161377560740.92036203048864.8583714323109.192826175138.537825777
22.53058250063-1.15088339228-1.576551035495.371523307363.03092175815.70280033674-0.114989545933-0.256528430724-0.3650989554480.6773607728520.45984871072-0.2647218596140.04803296775120.561437960946-0.3694373147750.779114070535-0.0749926988201-0.08749030700460.574456521526-0.01241200859940.8380272953379.3294568959103.930693166139.659834266
36.20847937996-2.215658378430.7532313670455.883000583590.7587039968951.440300800030.0722223595322-0.6305385514990.1069196191240.771259440139-0.5175150412611.07421430020.439759924122-1.114620245770.5407768400750.831119506557-0.1157492465310.2356062781750.76117180989-0.05693186347390.79668025139163.6322673361115.813224135146.474567388
40.983732350999-1.33675530745-0.002880422800455.231274303664.785284537386.57513039174-0.206266897283-0.2084916399780.148334420382-0.2355641619170.561034495071-0.566724386584-0.4938339182910.585959810377-0.4439743291930.679981704401-0.1131935691470.05076213042470.59552372542-0.08874416908340.8084601111176.1928562583115.063247916139.350891169
53.54120857094-3.958330518411.423875305464.6852382672-2.355566044222.739069159170.08077878861470.5559209241630.218947963267-0.5298430140130.0711426954633-0.496320115394-0.2020086203060.16206500051-0.2380169551870.397700691347-0.1036519047420.1464245122750.538645139817-0.1709495662120.69093603061678.3329581536103.382950895122.188988445
64.2497132392-5.1240215751.447609660748.2753157348-1.73153590722.72261916536-0.4605028936190.0652733590673-0.03560077908580.32058335770.5997529388210.201708371905-0.733064194508-0.306517735865-0.2132941212370.6998405079930.0514145985630.1273909136140.7454067664510.05203217707270.708281467755.6836069287103.801654349110.01850014
73.65247592637-2.811422394961.623024557156.36844863475-0.3612345804885.88517073530.4754395524940.677798759747-0.52183712801-1.26586011550.1859259024610.8407468680090.613099119402-0.244845480792-0.5510467134720.5544101752210.032452711899-0.0007912819765880.900395308402-0.06816810316820.75548649176962.479666502791.453296251499.4123534801
83.5285730878-0.6870898434190.6831635590544.86989350727-1.280015281143.94713046879-0.1032113025310.2145588927650.1734459975050.2135731440510.069352692976-0.0125011987269-0.309594281345-0.02031893217730.02631870481070.4675743810130.01245329057710.08394571407230.5619799254040.001704664160480.51985051769464.6856875748100.612174131108.218201214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 117 )
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 182 )
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 211 )
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 61 )
7X-RAY DIFFRACTION7chain 'B' and (resid 62 through 108 )
8X-RAY DIFFRACTION8chain 'B' and (resid 109 through 212 )

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