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- PDB-6cf8: Crystal structure of Cj0843 lytic transglycosylase of Campylobact... -

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Basic information

Entry
Database: PDB / ID: 6cf8
TitleCrystal structure of Cj0843 lytic transglycosylase of Campylobacter jejuni at 1.87A resolution
ComponentsLytic transglycosylase
KeywordsHYDROLASE
Function / homology:
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
Authorsvan den Akker, F. / Kumar, V. / Vijayaraghavan, J.
CitationJournal: PLoS ONE / Year: 2018
Title: Structural studies and molecular dynamics simulations suggest a processive mechanism of exolytic lytic transglycosylase from Campylobacter jejuni.
Authors: Vijayaraghavan, J. / Kumar, V. / Krishnan, N.P. / Kaufhold, R.T. / Zeng, X. / Lin, J. / van den Akker, F.
History
DepositionFeb 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lytic transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1608
Polymers61,4871
Non-polymers6727
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.640, 74.640, 194.086
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1209-

HOH

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Components

#1: Protein Lytic transglycosylase


Mass: 61487.293 Da / Num. of mol.: 1 / Fragment: residues 18-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: BD28_04025 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L7J388
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M lithium sulfate, 0.1 M Tris pH 8.0, and 39% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.87→64.7 Å / Num. obs: 51659 / % possible obs: 98.3 % / Redundancy: 19 % / Net I/σ(I): 16.3
Reflection shellResolution: 1.87→1.92 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→64.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.574 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.143
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 2493 4.8 %RANDOM
Rwork0.191 ---
obs0.1934 49078 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.08 Å2 / Biso mean: 42.006 Å2 / Biso min: 22.12 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.87→64.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 35 409 4669
Biso mean--70.85 45.54 -
Num. residues----510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024366
X-RAY DIFFRACTIONr_bond_other_d0.0020.024154
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9685894
X-RAY DIFFRACTIONr_angle_other_deg0.92839573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1645510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33224.931217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02515806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9271516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024877
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021041
LS refinement shellResolution: 1.874→1.922 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 158 -
Rwork0.279 3017 -
all-3175 -
obs--83.12 %

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