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- PDB-6xyz: Crystal structure of the GH18 chitinase ChiB from the chitin util... -

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Basic information

Entry
Database: PDB / ID: 6xyz
TitleCrystal structure of the GH18 chitinase ChiB from the chitin utilization locus of Flavobacterium johnsoniae
ComponentsCandidate chitinase Glycoside hydrolase family 18
KeywordsHYDROLASE / Chitinase GH18 Chitin ChiB
Function / homology
Function and homology information


chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
FORMIC ACID / Candidate chitinase Glycoside hydrolase family 18
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsMazurkewich, S. / Helland, R. / MacKenzie, A. / Eijsink, V. / Pope, P. / Branden, G. / Larsbrink, J.
Funding support Sweden, Norway, European Union, 3items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Norwegian Research Council247732 Norway
European Research Council (ERC)336355European Union
CitationJournal: Sci Rep / Year: 2020
Title: Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae.
Authors: Mazurkewich, S. / Helland, R. / Mackenzie, A. / Eijsink, V.G.H. / Pope, P.B. / Branden, G. / Larsbrink, J.
History
DepositionJan 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Candidate chitinase Glycoside hydrolase family 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7785
Polymers36,5461
Non-polymers2324
Water6,089338
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint4 kcal/mol
Surface area13530 Å2
Unit cell
Length a, b, c (Å)43.910, 66.440, 53.440
Angle α, β, γ (deg.)90.000, 98.307, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Candidate chitinase Glycoside hydrolase family 18


Mass: 36545.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (bacteria)
Gene: Fjoh_4560 / Production host: Escherichia coli (E. coli) / References: UniProt: A5FB54
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.15 M magnesium formate and 15% PEG3550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.63→36.36 Å / Num. obs: 34484 / % possible obs: 90.73 % / Redundancy: 4.7 % / Biso Wilson estimate: 18.88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04299 / Rpim(I) all: 0.02227 / Rrim(I) all: 0.04855 / Net I/σ(I): 19.71
Reflection shellResolution: 1.63→1.688 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.2067 / Mean I/σ(I) obs: 6.25 / Num. unique obs: 2962 / CC1/2: 0.955 / Rpim(I) all: 0.1048 / Rrim(I) all: 0.2321 / % possible all: 77.85

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
PHENIX1.15.2_3472refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FND

3fnd


Resolution: 1.63→36.36 Å / SU ML: 0.1449 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.8181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1887 2000 5.8 %
Rwork0.157 32470 -
obs0.1588 34470 90.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.59 Å2
Refinement stepCycle: LAST / Resolution: 1.63→36.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2443 0 15 338 2796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562600
X-RAY DIFFRACTIONf_angle_d0.78173528
X-RAY DIFFRACTIONf_chiral_restr0.0552383
X-RAY DIFFRACTIONf_plane_restr0.0048460
X-RAY DIFFRACTIONf_dihedral_angle_d20.9852950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.670.21251140.17971839X-RAY DIFFRACTION72.6
1.67-1.720.23631440.18042340X-RAY DIFFRACTION91.59
1.72-1.770.24311460.18232365X-RAY DIFFRACTION93.28
1.77-1.820.23311470.18392392X-RAY DIFFRACTION93.97
1.82-1.890.24241470.17662390X-RAY DIFFRACTION93.69
1.89-1.960.22191460.17812368X-RAY DIFFRACTION93.39
1.96-2.050.23481460.16532375X-RAY DIFFRACTION93.13
2.05-2.160.22421460.16342370X-RAY DIFFRACTION93.15
2.16-2.30.21161460.16192375X-RAY DIFFRACTION92.34
2.3-2.470.19061420.16412312X-RAY DIFFRACTION90.99
2.47-2.720.21421390.1672262X-RAY DIFFRACTION88.3
2.72-3.120.17951260.16452030X-RAY DIFFRACTION79.35
3.12-3.930.16871550.14962511X-RAY DIFFRACTION97.58
3.93-36.360.14361560.13122541X-RAY DIFFRACTION96.81

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