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- PDB-5zzu: Crystal structure of the C-terminal periplasmic domain of EcEptC ... -

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Basic information

Entry
Database: PDB / ID: 5zzu
TitleCrystal structure of the C-terminal periplasmic domain of EcEptC from Escherichia coli- complex with Zn
ComponentsPhosphoethanolamine transferase EptC
KeywordsTRANSFERASE / Phosphoethanolamine transferases
Function / homology
Function and homology information


phosphotransferase activity, phosphate group as acceptor / Transferases; Transferring phosphorus-containing groups / lipopolysaccharide core region biosynthetic process / sulfuric ester hydrolase activity / integral component of membrane / plasma membrane
Similarity search - Function
Phosphoethanolamine transferase / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Phosphoethanolamine transferase EptC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhao, Y.Q. / Cheng, W. / Gu, Y.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570842 China
CitationJournal: To Be Published
Title: Structural and mechanistic insights into polymyxin resistance mediated by EptC originating from Escherichia coli
Authors: Zhao, Y.Q. / Lai, Y.J. / Zhou, D. / Dou, C. / Gu, Y.J. / Nie, C.L. / Wei, Y.Q. / Cheng, W.
History
DepositionJun 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoethanolamine transferase EptC
B: Phosphoethanolamine transferase EptC
C: Phosphoethanolamine transferase EptC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,2136
Polymers138,0163
Non-polymers1963
Water11,980665
1
A: Phosphoethanolamine transferase EptC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0712
Polymers46,0051
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area14590 Å2
MethodPISA
2
B: Phosphoethanolamine transferase EptC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0712
Polymers46,0051
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area14810 Å2
MethodPISA
3
C: Phosphoethanolamine transferase EptC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0712
Polymers46,0051
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area14610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.060, 85.060, 121.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Phosphoethanolamine transferase EptC


Mass: 46005.461 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: eptC, cptA, yijP, b3955, JW3927 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0CB39, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 1.84 Å3/Da / Density % sol: 33.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium formate (pH7.5), 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Mar 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.1→46.83 Å / Num. obs: 56697 / % possible obs: 98.72 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.03 / Rrim(I) all: 0.094 / Net I/σ(I): 17.6
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 5.48 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5219 / CC1/2: 0.887 / Rpim(I) all: 0.196 / Rrim(I) all: 0.472 / % possible all: 90.11

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZNV

5znv
PDB Unreleased entry


Resolution: 2.1→46.83 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.72
RfactorNum. reflection% reflection
Rfree0.1973 2823 4.99 %
Rwork0.1646 --
obs0.1662 56607 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8676 0 3 665 9344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058912
X-RAY DIFFRACTIONf_angle_d0.77612147
X-RAY DIFFRACTIONf_dihedral_angle_d12.8885340
X-RAY DIFFRACTIONf_chiral_restr0.0481292
X-RAY DIFFRACTIONf_plane_restr0.0051606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13620.26231220.21022426X-RAY DIFFRACTION88
2.1362-2.17510.23241440.19252506X-RAY DIFFRACTION92
2.1751-2.21690.26371810.20142554X-RAY DIFFRACTION96
2.2169-2.26220.25961350.20432668X-RAY DIFFRACTION99
2.2622-2.31130.24851420.18882725X-RAY DIFFRACTION100
2.3113-2.36510.19581240.17332795X-RAY DIFFRACTION100
2.3651-2.42420.24051580.17392707X-RAY DIFFRACTION100
2.4242-2.48980.20351400.17232707X-RAY DIFFRACTION100
2.4898-2.5630.23131400.17582715X-RAY DIFFRACTION100
2.563-2.64580.20091240.18092784X-RAY DIFFRACTION100
2.6458-2.74030.22941080.17652729X-RAY DIFFRACTION100
2.7403-2.850.22621160.18292763X-RAY DIFFRACTION100
2.85-2.97970.22751160.17862725X-RAY DIFFRACTION100
2.9797-3.13680.20941580.18112707X-RAY DIFFRACTION100
3.1368-3.33330.1991280.17512726X-RAY DIFFRACTION100
3.3333-3.59050.18641550.16492728X-RAY DIFFRACTION100
3.5905-3.95170.18391680.15012672X-RAY DIFFRACTION100
3.9517-4.52310.15541520.1282725X-RAY DIFFRACTION100
4.5231-5.69710.1491340.12832746X-RAY DIFFRACTION100
5.6971-46.84290.17391780.1572676X-RAY DIFFRACTION100

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