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- PDB-8xeh: Crystal structure of HEPN-MNT complex -

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Basic information

Entry
Database: PDB / ID: 8xeh
TitleCrystal structure of HEPN-MNT complex
Components
  • HEPN
  • MNT
KeywordsPROTEIN BINDING / HEPN-MNT module
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJin, C. / Jeon, C. / Kim, D.H. / Lee, B.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A5A2024425 Korea, Republic Of
National Research Foundation (NRF, Korea)2021R1F1A1050961 Korea, Republic Of
CitationJournal: To Be Published
Title: Structural and functional study of HEPN-MNT module from Legionella pneumophila
Authors: Jin, C. / Jeon, C. / Kim, D.H. / Lee, B.J.
History
DepositionDec 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: MNT
C: HEPN
D: HEPN
A: HEPN
B: HEPN


Theoretical massNumber of molelcules
Total (without water)77,4065
Polymers77,4065
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.563, 93.747, 84.958
Angle α, β, γ (deg.)90.000, 123.860, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein MNT


Mass: 12208.913 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein
HEPN


Mass: 16299.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: of 20% (w/v) PEG 3350, pH 7.0 and 0.2 M ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 28576 / % possible obs: 98.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.77 Å2 / CC1/2: 0.996 / Net I/σ(I): 20.33
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 1433 / CC1/2: 0.847

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Processing

Software
NameVersionClassification
PHENIX1.20rc4_4418refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.15 Å / SU ML: 0.3434 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7311
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 1998 7.21 %
Rwork0.2031 25728 -
obs0.2062 27726 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 0 148 5252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245207
X-RAY DIFFRACTIONf_angle_d0.45257017
X-RAY DIFFRACTIONf_chiral_restr0.0344755
X-RAY DIFFRACTIONf_plane_restr0.0033907
X-RAY DIFFRACTIONf_dihedral_angle_d4.0805668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.37561340.2881723X-RAY DIFFRACTION89.41
2.46-2.520.30861350.26421737X-RAY DIFFRACTION91.18
2.52-2.60.30571420.25391819X-RAY DIFFRACTION94.69
2.6-2.680.33191390.23911813X-RAY DIFFRACTION93.98
2.68-2.780.31591400.22621802X-RAY DIFFRACTION94.73
2.78-2.890.28181430.25841840X-RAY DIFFRACTION96.26
2.89-3.020.31021440.25941862X-RAY DIFFRACTION96.16
3.02-3.180.3091420.25171813X-RAY DIFFRACTION94.58
3.18-3.380.25931440.21521860X-RAY DIFFRACTION96.44
3.38-3.640.23191480.1951898X-RAY DIFFRACTION98.46
3.64-4.010.22031470.17341888X-RAY DIFFRACTION98.45
4.01-4.590.20051460.16751896X-RAY DIFFRACTION97.84
4.59-5.780.20831460.16981878X-RAY DIFFRACTION96.66
5.78-47.150.20131480.17431899X-RAY DIFFRACTION95.65
Refinement TLS params.Method: refined / Origin x: 18.9439135781 Å / Origin y: 7.66973520037 Å / Origin z: 17.1932989572 Å
111213212223313233
T0.318279389438 Å20.0618014874118 Å2-0.00609811197477 Å2-0.159751518766 Å2-0.00504292440283 Å2--0.308876945059 Å2
L1.29037319783 °2-0.48613369416 °20.710632964582 °2-0.620501541006 °2-0.31656428462 °2--1.12148507045 °2
S0.142420798181 Å °0.0981016671203 Å °-0.0130448537645 Å °-0.0819130936663 Å °-0.0751872291494 Å °-0.00892904628369 Å °0.0391501967872 Å °0.0574148789114 Å °-0.042668916307 Å °
Refinement TLS groupSelection details: all

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