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- PDB-6p5h: Structure of MavC middle insertion domain -

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Basic information

Entry
Database: PDB / ID: 6p5h
TitleStructure of MavC middle insertion domain
ComponentsMavC
KeywordsPROTEIN BINDING / UbE2N / Effector / MavC
Function / homology: / MvcA insertion domain / Uncharacterized protein / MvcA insertion domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsNegron Teron, K.I. / Puvar, K. / Iyer, S. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM126296-02 United States
CitationJournal: Nat Commun / Year: 2020
Title: Legionella effector MavC targets the Ube2N~Ub conjugate for noncanonical ubiquitination.
Authors: Puvar, K. / Iyer, S. / Fu, J. / Kenny, S. / Negron Teron, K.I. / Luo, Z.Q. / Brzovic, P.S. / Klevit, R.E. / Das, C.
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MavC
B: MavC


Theoretical massNumber of molelcules
Total (without water)24,4982
Polymers24,4982
Non-polymers00
Water6,503361
1
A: MavC


Theoretical massNumber of molelcules
Total (without water)12,2491
Polymers12,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MavC


Theoretical massNumber of molelcules
Total (without water)12,2491
Polymers12,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.027, 52.027, 79.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein MavC


Mass: 12248.795 Da / Num. of mol.: 2 / Fragment: middle insertion domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_10720 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F4I5, UniProt: Q5ZTL4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 2 M ammonium sulfate, 0.2 M lithium sulfate, 0.1 M CAPS: NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978772 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978772 Å / Relative weight: 1
ReflectionResolution: 1.53→39.229 Å / Num. obs: 36418 / % possible obs: 99.96 % / Redundancy: 8.2 % / Net I/σ(I): 24.9
Reflection shellResolution: 1.53→1.585 Å / Num. unique obs: 3636 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TSC

5tsc


Resolution: 1.53→39.229 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 24.66
RfactorNum. reflection% reflection
Rfree0.224 2005 5.51 %
Rwork0.1986 --
obs0.2 36384 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.53→39.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 0 361 1981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061652
X-RAY DIFFRACTIONf_angle_d0.8072228
X-RAY DIFFRACTIONf_dihedral_angle_d2.9391014
X-RAY DIFFRACTIONf_chiral_restr0.054238
X-RAY DIFFRACTIONf_plane_restr0.005292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5302-1.56850.25261440.24462419X-RAY DIFFRACTION100
1.5685-1.61090.29441440.24692469X-RAY DIFFRACTION100
1.6109-1.65830.29661460.23572455X-RAY DIFFRACTION100
1.6583-1.71180.24771380.22912448X-RAY DIFFRACTION100
1.7118-1.7730.29831410.2342476X-RAY DIFFRACTION100
1.773-1.8440.26391390.22862448X-RAY DIFFRACTION100
1.844-1.92790.30641410.22472490X-RAY DIFFRACTION100
1.9279-2.02950.25391400.20752424X-RAY DIFFRACTION100
2.0295-2.15670.22531440.20612485X-RAY DIFFRACTION100
2.1567-2.32320.21051380.19832447X-RAY DIFFRACTION100
2.3232-2.55690.25031460.19922468X-RAY DIFFRACTION100
2.5569-2.92680.2081480.19962449X-RAY DIFFRACTION100
2.9268-3.68710.18431500.18412452X-RAY DIFFRACTION100
3.6871-39.2420.20021460.17192449X-RAY DIFFRACTION100

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