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- PDB-6cfc: Crystal structure of soluble lytic transglycosylase Cj0843 of Cam... -

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Basic information

Entry
Database: PDB / ID: 6cfc
TitleCrystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni in complex with Bulgecin A
ComponentsLytic transglycosylase
KeywordsHYDROLASE
Function / homologyChem-BLG / :
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
Authorsvan den Akker, F. / Kumar, V.
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 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 4, 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

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Assembly

Deposited unit
A: Lytic transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,89011
Polymers61,4731
Non-polymers1,41710
Water5,242291
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)74.294, 74.294, 190.461
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Lytic transglycosylase


Mass: 61473.270 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-BLG / 4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE / BULGECIN A


Mass: 552.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H30N3O14S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5 and 25% (w/v) PEG 3350. Bulgecin A was soaked into the crystal at 2.4mM concentration for 40 min at room temperature prior to freezing the crystal

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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: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.04→64.34 Å / Num. obs: 39342 / % possible obs: 99.1 % / Redundancy: 5.7 % / Net I/σ(I): 11.6
Reflection shellResolution: 2.04→2.09 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CF8

6cf8


Resolution: 2.04→64.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.469 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.16
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 1920 4.9 %RANDOM
Rwork0.1773 ---
obs0.1793 37371 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.77 Å2 / Biso mean: 42.486 Å2 / Biso min: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.04→64.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4192 0 80 291 4563
Biso mean--54.4 47.91 -
Num. residues----506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024389
X-RAY DIFFRACTIONr_bond_other_d0.0030.024169
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9775931
X-RAY DIFFRACTIONr_angle_other_deg0.9773.0039613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.275508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12724.908218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07815808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5951517
X-RAY DIFFRACTIONr_chiral_restr0.0790.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021042
LS refinement shellResolution: 2.041→2.094 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 167 -
Rwork0.244 2683 -
all-2850 -
obs--99.55 %

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