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- PDB-7f2a: Crystal structure of Neisseria meningitidis EarP bound TDP -

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Basic information

Entry
Database: PDB / ID: 7f2a
TitleCrystal structure of Neisseria meningitidis EarP bound TDP
ComponentsElongation factor P maturation arginine rhamnosyltransferase EarP
KeywordsTRANSFERASE / EarP / TDP / Neisseria meningitidis
Function / homologyprotein-arginine rhamnosyltransferase activity / Protein-arginine rhamnosyltransferase EarP / Elongation-Factor P (EF-P) rhamnosyltransferase EarP / translation elongation factor activity / THYMIDINE-5'-DIPHOSPHATE / Protein-arginine rhamnosyltransferase
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 Å
AuthorsYoo, Y.
CitationJournal: To Be Published
Title: Crystal structure of Neisseria meningitidis EarP bound TDP
Authors: Yoo, Y.
History
DepositionJun 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)89,3378
Polymers88,1482
Non-polymers1,1896
Water1086
1
A: Elongation factor P maturation arginine rhamnosyltransferase EarP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7645
Polymers44,0741
Non-polymers6904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-18 kcal/mol
Surface area16350 Å2
MethodPISA
2
F: Elongation factor P maturation arginine rhamnosyltransferase EarP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5723
Polymers44,0741
Non-polymers4982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-19 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.855, 125.287, 128.278
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-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.28 %
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: 2.58→45.66 Å / Num. obs: 25556 / % possible obs: 99.88 % / Redundancy: 10.7 % / Biso Wilson estimate: 41.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Net I/σ(I): 23.09
Reflection shellResolution: 2.58→2.672 Å / Rmerge(I) obs: 0.7574 / Mean I/σ(I) obs: 3.67 / Num. unique obs: 2479 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.58→45.66 Å / SU ML: 0.3714 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.2957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2694 3722 7.78 %
Rwork0.2157 44093 -
obs0.2198 25546 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.15 Å2
Refinement stepCycle: LAST / Resolution: 2.58→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 0 70 6 6198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016382
X-RAY DIFFRACTIONf_angle_d1.19138700
X-RAY DIFFRACTIONf_chiral_restr0.0675898
X-RAY DIFFRACTIONf_plane_restr0.00751118
X-RAY DIFFRACTIONf_dihedral_angle_d18.11932270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.610.40351430.30241600X-RAY DIFFRACTION99.89
2.61-2.650.32151390.26981626X-RAY DIFFRACTION100
2.65-2.680.29981350.27841673X-RAY DIFFRACTION100
2.68-2.720.34981430.27711635X-RAY DIFFRACTION99.83
2.72-2.760.38321500.2921591X-RAY DIFFRACTION100
2.76-2.810.30591360.27761632X-RAY DIFFRACTION99.89
2.81-2.850.37421380.28391660X-RAY DIFFRACTION100
2.85-2.90.37771240.28751642X-RAY DIFFRACTION100
2.9-2.950.34681410.2651594X-RAY DIFFRACTION100
2.95-3.010.31941390.28051672X-RAY DIFFRACTION100
3.01-3.070.35571360.27171626X-RAY DIFFRACTION100
3.07-3.140.33531300.25771633X-RAY DIFFRACTION100
3.14-3.210.3191500.25411654X-RAY DIFFRACTION100
3.21-3.290.32271350.24061621X-RAY DIFFRACTION99.89
3.29-3.380.28371300.23081622X-RAY DIFFRACTION100
3.38-3.480.28031370.23261649X-RAY DIFFRACTION100
3.48-3.590.29251420.21151616X-RAY DIFFRACTION100
3.59-3.720.28131340.21511674X-RAY DIFFRACTION100
3.72-3.870.23161360.20091608X-RAY DIFFRACTION100
3.87-4.050.22071320.18511662X-RAY DIFFRACTION100
4.05-4.260.22821440.17451614X-RAY DIFFRACTION100
4.26-4.530.19961250.16291654X-RAY DIFFRACTION100
4.53-4.870.18881460.15641630X-RAY DIFFRACTION100
4.87-5.360.20441410.16981633X-RAY DIFFRACTION100
5.36-6.140.29711510.20611626X-RAY DIFFRACTION100
6.14-7.720.21341320.20391625X-RAY DIFFRACTION100
7.73-45.660.22541330.1851621X-RAY DIFFRACTION98.48

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