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- PDB-5j90: Structure of Fjoh_4558, a chitin-binding SusD homolog from Flavob... -

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Basic information

Entry
Database: PDB / ID: 5j90
TitleStructure of Fjoh_4558, a chitin-binding SusD homolog from Flavobacterium johnsoniae
ComponentsRagB/SusD domain protein
KeywordsChitin-binding protein / Chitin-binding / SusD homolog / Bacteroidetes / Flavobacterium johnsoniae
Function / homologySusD-like / Susd and RagB outer membrane lipoprotein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / RagB/SusD domain protein
Function and homology information
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3932 Å
AuthorsKoropatkin, N.M.
CitationJournal: Biotechnol Biofuels / Year: 2016
Title: A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin.
Authors: Larsbrink, J. / Zhu, Y. / Kharade, S.S. / Kwiatkowski, K.J. / Eijsink, V.G. / Koropatkin, N.M. / McBride, M.J. / Pope, P.B.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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: RagB/SusD domain protein
B: RagB/SusD domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,84713
Polymers113,1642
Non-polymers68311
Water27,2751514
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint28 kcal/mol
Surface area32090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.331, 112.137, 121.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RagB/SusD domain protein


Mass: 56582.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101 / Gene: Fjoh_4558 / Plasmid: pETite N-his / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: A5FB66
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1514 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 150 mM Tris-HCl pH 8.5, 27% sokolan CP5. These crystals were briefly soaked in 10mM acetylchitopentaose prior to freezing with a solution of 20% ethylene glycol, 80% crystallization media
Temp details: room temp

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen vapor
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 30, 2015
RadiationMonochromator: 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 215603 / % possible obs: 99.2 % / Redundancy: 7.9 % / Biso Wilson estimate: 11.53 Å2 / Rmerge(I) obs: 0.056 / Net I/av σ(I): 44.733 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.39-1.415.90.364183.6
1.41-1.446.40.327199.7
1.44-1.476.80.272199.8
1.47-1.57.60.2331100
1.5-1.537.80.211100
1.53-1.577.90.181100
1.57-1.67.90.151100
1.6-1.657.90.1361100
1.65-1.780.1171100
1.7-1.7580.1071100
1.75-1.818.10.0991100
1.81-1.898.20.0931100
1.89-1.978.30.0831100
1.97-2.088.30.071100
2.08-2.218.40.0631100
2.21-2.388.40.0651100
2.38-2.628.40.0621100
2.62-2.998.40.0571100
2.99-3.778.30.0341100
3.77-5080.03199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F7A

4f7a


Resolution: 1.3932→36.574 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.04
RfactorNum. reflection% reflection
Rfree0.1673 1996 0.93 %
Rwork0.1503 --
obs0.1504 215458 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.9 Å2 / Biso mean: 15.7941 Å2 / Biso min: 5.75 Å2
Refinement stepCycle: final / Resolution: 1.3932→36.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7534 0 110 1514 9158
Biso mean--26.74 26.36 -
Num. residues----964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067820
X-RAY DIFFRACTIONf_angle_d1.08410600
X-RAY DIFFRACTIONf_chiral_restr0.0721119
X-RAY DIFFRACTIONf_plane_restr0.0051378
X-RAY DIFFRACTIONf_dihedral_angle_d11.5722816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3932-1.4280.2331380.1935147981493698
1.428-1.46660.20731350.17871513515270100
1.4666-1.50980.18871570.17041511015267100
1.5098-1.55850.19471370.16191519615333100
1.5585-1.61420.17561400.15421513215272100
1.6142-1.67890.16831440.15271517115315100
1.6789-1.75530.15811410.15161520115342100
1.7553-1.84780.14341300.15541522015350100
1.8478-1.96360.15131580.15791525215410100
1.9636-2.11520.18071370.15191525715394100
2.1152-2.3280.18531430.15071530815451100
2.328-2.66480.17481430.15421535415497100
2.6648-3.3570.17281460.151545215598100
3.357-36.58660.14041470.13031587616023100

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