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- PDB-7vch: Crystal structure of Neisseria meningitidis EarP bound TDP-L-Rhamnose -

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Basic information

Entry
Database: PDB / ID: 7vch
TitleCrystal structure of Neisseria meningitidis EarP bound TDP-L-Rhamnose
ComponentsElongation factor P maturation arginine rhamnosyltransferase EarP
KeywordsTRANSFERASE / EarP / TDPR / Neisseria meningitidis
Function / homologyprotein-arginine rhamnosyltransferase activity / Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / translation elongation factor activity / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / Protein-arginine rhamnosyltransferase
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsYoo, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Neisseria meningitidis EarP bound TDP-L-Rhamnose
Authors: Yoo, Y.
History
DepositionSep 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor P maturation arginine rhamnosyltransferase EarP
F: Elongation factor P maturation arginine rhamnosyltransferase EarP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7259
Polymers88,1482
Non-polymers1,5777
Water00
1
A: Elongation factor P maturation arginine rhamnosyltransferase EarP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9105
Polymers44,0741
Non-polymers8374
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Elongation factor P maturation arginine rhamnosyltransferase EarP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8144
Polymers44,0741
Non-polymers7403
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.407, 124.402, 127.647
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 Elongation factor P maturation arginine rhamnosyltransferase EarP / Uncharacterized protein conserved in bacteria


Mass: 44073.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria)
Gene: earP, CNQ34_12095, ERS040961_00525, ERS514851_01386, H7969_05560, JY21_02145, NMA510612_1261
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X5EQ00
#2: Chemical ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N2O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium cacodylate pH6.5, 1.26M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→44.55 Å / Num. obs: 18268 / % possible obs: 99.55 % / Redundancy: 5.4 % / Biso Wilson estimate: 76.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1128 / Net I/σ(I): 12.26
Reflection shellResolution: 2.85→2.952 Å / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 1798 / CC1/2: 0.642

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→44.55 Å / SU ML: 0.4995 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.4198
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3091 1517 4.52 %
Rwork0.2254 32061 -
obs0.2291 18259 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.91 Å2
Refinement stepCycle: LAST / Resolution: 2.85→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 0 95 0 6217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00986408
X-RAY DIFFRACTIONf_angle_d1.28058740
X-RAY DIFFRACTIONf_chiral_restr0.3072912
X-RAY DIFFRACTIONf_plane_restr0.00661118
X-RAY DIFFRACTIONf_dihedral_angle_d22.40642314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.940.34871470.32852935X-RAY DIFFRACTION99.77
2.94-3.050.40381300.33092932X-RAY DIFFRACTION99.8
3.05-3.170.41261450.31162987X-RAY DIFFRACTION99.33
3.17-3.310.35621320.29092904X-RAY DIFFRACTION99.12
3.31-3.490.35471410.25372913X-RAY DIFFRACTION98.58
3.49-3.710.5031200.26462877X-RAY DIFFRACTION96.93
3.71-3.990.32921440.23152940X-RAY DIFFRACTION99.07
3.99-4.390.29411370.20732873X-RAY DIFFRACTION98.05
4.39-5.030.30941390.18332881X-RAY DIFFRACTION98.08
5.03-6.330.2361440.21382931X-RAY DIFFRACTION98.78
6.33-44.550.23131380.17912888X-RAY DIFFRACTION97.68

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