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- PDB-8co2: YdaS N-terminal domain from prophage CP-933P in E. coli O157:H7 -

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Basic information

Entry
Database: PDB / ID: 8co2
TitleYdaS N-terminal domain from prophage CP-933P in E. coli O157:H7
ComponentsPutative antirepressor protein Cro
KeywordsDNA BINDING PROTEIN / Cro repressor / cryptic prophage / antitoxin
Function / homologyBacterial antitoxin YdaS / Bacterial toxin YdaS / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / ISOPROPYL ALCOHOL / Putative antirepressor protein Cro
Function and homology information
Biological speciesEscherichia coli O157 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6388072348 Å
AuthorsProlic-Kalinsek, M. / Loris, R.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G.0033.20N Belgium
Research Foundation - Flanders (FWO)G.0226.17N Belgium
CitationJournal: To Be Published
Title: YdaS from the Escherichia coli cryptic prophage CP-933P forms an evolutionary link between Cro repressors and HigA antitoxins
Authors: Prolic-Kalinsek, M. / Volkov, A.N. / Hadzi, S. / Bervoets, I. / Loris, R.
History
DepositionFeb 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative antirepressor protein Cro
B: Putative antirepressor protein Cro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2264
Polymers21,0702
Non-polymers1562
Water1,38777
1
A: Putative antirepressor protein Cro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6312
Polymers10,5351
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative antirepressor protein Cro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5952
Polymers10,5351
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.710, 42.710, 65.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein Putative antirepressor protein Cro


Mass: 10534.940 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157 (bacteria) / Gene: A2F99_004475 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D7C0Q9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.024 M 1,6-Hexanediol, 0.024 M 1-Butanol, 0.024 M 1,2-Propanediol, 0.024 M 2-Propanol 0.024 M 1,3-Propanediol, 0.05 M Sodium HEPES, 0.05 M MOPS, 9.375% v/v MPD; 9.375% PEG 1000; 9.375% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.6388072348→36.9879449956 Å / Num. obs: 16212 / % possible obs: 99.4 % / Redundancy: 10.44 % / Biso Wilson estimate: 43.4269937054 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.81
Reflection shellResolution: 1.6388072348→1.75 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.135 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 2549 / CC1/2: 0.668 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6388072348→36.9879449956 Å / SU ML: 0.264915240595 / Cross valid method: FREE R-VALUE / σ(F): 1.95891869141 / Phase error: 31.735679893
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.257643008052 810 4.99629903775 %
Rwork0.211857012744 15402 -
obs0.214110437676 16212 99.3991416309 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.8461060216 Å2
Refinement stepCycle: LAST / Resolution: 1.6388072348→36.9879449956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 9 77 1224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005148885634581173
X-RAY DIFFRACTIONf_angle_d0.7443780570751593
X-RAY DIFFRACTIONf_chiral_restr0.0439878137398179
X-RAY DIFFRACTIONf_plane_restr0.00429057527795202
X-RAY DIFFRACTIONf_dihedral_angle_d16.6246554693704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6388072348-1.74150.384313226631300.3611362666262488X-RAY DIFFRACTION96.5695315382
1.7415-1.87590.3174204837841350.3026858354692574X-RAY DIFFRACTION99.963099631
1.8759-2.06470.30756225011370.2672910781122597X-RAY DIFFRACTION100
2.0647-2.36340.2554702632161360.2321746404672588X-RAY DIFFRACTION100
2.3634-2.97750.2655662287711360.2469162799452579X-RAY DIFFRACTION100
2.9775-36.98794499560.2434464401271360.1840049576372576X-RAY DIFFRACTION99.852724595
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)
12.75233950451-1.86986497507-3.688213075963.161435377421.152591114236.58469021189-0.422731215195-1.871464364790.0361558596360.3708872761960.4573402592190.8474063154040.742030712416-1.522096147630.2752646351780.3130620302120.0123146306275-0.001967048102170.905381312992-0.09959861007070.419268936543-16.2926309273-6.270903762766.61031893012
28.66977521141-4.56634386586-2.714574273213.42706666211-0.5036348766235.53571326612-0.1355646985610.09418010613890.817815388216-0.5123496270250.326698322097-0.569233864553-0.0797868395748-0.349025787884-0.2189447009030.396455874755-0.159237162099-0.01242167442560.645090657834-0.03432458396930.513846301076-14.05035710840.690631872851-2.48165424392
34.98694530481-2.76330291650.9765821737069.72337147971-1.021182106378.97986956733-0.5944198803540.254500867491-0.427857433255-0.2303780297790.857834771205-0.6404646116350.1864749909120.223612819079-0.2067608576230.315310447415-0.1288377463670.01407193285940.614397224484-0.1668704944760.395335573438-6.31778322915-8.909799213910.10492520064
49.28122626237.493047316462.908281872187.206629741634.814277423986.6818265816-0.386312149938-1.81313093353-0.6373673093310.6416844428631.54803199395-3.028170934782.528691330380.969156393686-0.555675087520.3072269547430.128341863822-0.0006359276786491.34070922317-0.4788358798391.146693053082.73681732157-16.27455008871.4300329687
54.27006668433-4.09691410599-0.6345949163184.121455901390.397169582944.92373324045-0.69172517649-1.142020105330.5913526120361.091645377850.908608889861-0.956850059033-1.150580663080.864678038285-0.3420862388370.4827069706290.0124281060565-0.005158677402510.748507050328-0.0412870360690.42190707502113.19008975918.933934784825.99364988525
68.96362954082-6.163814085232.563912456914.31470704737-0.1562552494159.863805971320.364351628812-0.340265480447-0.544395137394-0.5476277938070.1559143671730.2536347404650.00491252958229-0.0327993589378-0.4292060517010.330026969486-0.0567762046859-0.01342539835830.51221327416-0.01634126228830.3516130187411.00237631680.764902103858-1.82533148889
77.23857935063-2.928129917040.3602669603024.266261617764.367932835416.85840288821-0.205260472455-0.01278186998270.35374888821-0.3174182418840.1698567421090.312885875875-0.6148651714580.2233206049160.06643994396660.403770742747-0.0391789981158-0.04193976011820.5496666785330.09025332353390.4466206407932.8966032314410.29371770920.773053059582
86.167386864894.418098726950.6138207604459.8697026245-1.24409694860.505775848488-0.762557585793-1.398330335992.71909058963-0.474007255587-0.6559082558654.34712934655-1.70053410399-1.864966520181.650021991040.5877049281310.194335494201-0.2975675773610.989238805911-0.2249004369411.55848946079-5.9634322614517.41054589533.45149751722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 33 )
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 64 )
4X-RAY DIFFRACTION4chain 'A' and (resid 65 through 74 )
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 11 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 33 )
7X-RAY DIFFRACTION7chain 'B' and (resid 34 through 64 )
8X-RAY DIFFRACTION8chain 'B' and (resid 65 through 75 )

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