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- PDB-7x9r: Crystal structure of the antirepressor GmaR -

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Basic information

Entry
Database: PDB / ID: 7x9r
TitleCrystal structure of the antirepressor GmaR
ComponentsGlycosyl transferase family 2
KeywordsPROTEIN BINDING / Antirepressor
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / TPR repeat profile. / Tetratricopeptide repeats / Nucleotide-diphospho-sugar transferases / Tetratricopeptide repeat / transferase activity / Tetratricopeptide-like helical domain superfamily / Glycosyl transferase family 2
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsCho, S.Y. / Na, H.W. / Oh, H.B. / Kwak, Y.M. / Song, W.S. / Park, S.C. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1002100 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural basis of flagellar motility regulation by the MogR repressor and the GmaR antirepressor in Listeria monocytogenes.
Authors: Cho, S.Y. / Na, H.W. / Oh, H.B. / Kwak, Y.M. / Song, W.S. / Park, S.C. / Jeon, W.J. / Cho, H. / Oh, B.C. / Park, J. / Kang, S.G. / Lee, G.S. / Yoon, S.I.
History
DepositionMar 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 29, 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: Glycosyl transferase family 2


Theoretical massNumber of molelcules
Total (without water)58,3011
Polymers58,3011
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22180 Å2
Unit cell
Length a, b, c (Å)74.736, 85.779, 104.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glycosyl transferase family 2 / Glycosyltransferase


Mass: 58300.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: AF006_02785, B1O25_01135, B4X79_02990, B4Y57_05390, F3O35_02795
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3A6YDN3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: sodium acetate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 32149 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 42.34 Å2 / CC1/2: 0.991 / Net I/σ(I): 19.7
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1542 / CC1/2: 0.495 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→29.59 Å / SU ML: 0.3029 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.4112
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2607 1660 5.17 %
Rwork0.2236 30430 -
obs0.2255 32090 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.89 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 0 52 3648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493678
X-RAY DIFFRACTIONf_angle_d0.61374994
X-RAY DIFFRACTIONf_chiral_restr0.0428555
X-RAY DIFFRACTIONf_plane_restr0.004648
X-RAY DIFFRACTIONf_dihedral_angle_d12.93852192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.320.3591120.32512410X-RAY DIFFRACTION95.13
2.32-2.390.33111420.3062463X-RAY DIFFRACTION98.6
2.39-2.480.35511420.32507X-RAY DIFFRACTION98.88
2.48-2.580.31671320.27462516X-RAY DIFFRACTION99.59
2.58-2.70.29951380.27322517X-RAY DIFFRACTION99.85
2.7-2.840.28041360.24362534X-RAY DIFFRACTION99.89
2.84-3.020.25811490.24892525X-RAY DIFFRACTION99.85
3.02-3.250.27571270.2432576X-RAY DIFFRACTION99.89
3.25-3.570.26751520.22742545X-RAY DIFFRACTION99.89
3.57-4.090.21661590.19832532X-RAY DIFFRACTION99.56
4.09-5.150.24041140.18092623X-RAY DIFFRACTION99.64
5.15-29.590.24011570.20082682X-RAY DIFFRACTION98.85
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)
14.28926319102-1.361624574453.480794997492.16673278794-2.059086114733.233497740760.600801682507-0.32623220086-0.379010092236-0.54984769048-0.04630197050430.6995318374430.934833079945-0.501354606286-0.5472587135790.732318249779-0.0351971211374-0.1534134512250.3773399459890.06828961680650.55478487031625.9078255781-6.7107284653563.5296026563
20.6888466793530.2215952492321.699513357882.662564860851.570339629477.396498062940.4034065698770.376997724768-0.46255958432-1.12015745948-0.07220374970210.4903025928850.939618444211-0.120387682286-0.3640716166340.7202263303460.0543357128733-0.3591880819350.4922052982530.00741052266680.76560684476416.26424486442.5696272488344.7803882822
32.500795534950.646494441845-1.178625905264.522559414863.635294422798.786440070180.294331297718-0.7441234780660.3142118659230.352975398859-0.528462219810.5599554044990.00440743539458-0.481903088150.1603588198660.248360265098-0.0636529627070.02317034922090.520402320926-0.07411863386330.42356008505310.851993533832.119870395268.6114017963
47.97918412543-4.154167268510.7134682282062.99498284274-0.7082691673150.5851326368060.2228662015110.127313214432-0.0360231998272-0.0209360767514-0.1870112233190.047790971852-0.281575011538-0.0617023400154-0.02506716054480.3343263229950.038910875498-0.01600751204080.239450749389-0.01502817368170.26313869626928.803483654420.509383172955.7417292437
50.9474575234810.267096144630.3392802185871.99397547864-0.7374651652733.415892251590.00929826168803-0.2894801966860.02721907270760.2866048104350.006200795066420.019870871126-0.252706812318-0.1762752960050.0104210489290.2733678254320.0719058847011-0.01029610362140.337404180494-0.0009712115954620.35276811720345.68077001367.2396522592779.4054534173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 519 through 598 )
2X-RAY DIFFRACTION2chain 'A' and (resid 599 through 630 )
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 267 )
4X-RAY DIFFRACTION4chain 'A' and (resid 268 through 346 )
5X-RAY DIFFRACTION5chain 'A' and (resid 347 through 518 )

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