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- PDB-6rw7: An AA10 LPMO from the shipworm symbiont Teredinibacter turnerae -

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Basic information

Entry
Database: PDB / ID: 6rw7
TitleAn AA10 LPMO from the shipworm symbiont Teredinibacter turnerae
ComponentsCarbohydrate binding module family 33 and 10 domain protein
KeywordsOXIDOREDUCTASE / Lytic Polysaccharide Monooxygenase / CAZY / AA10 / Cellulose
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / cellulose binding / carbohydrate metabolic process
Similarity search - Function
Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Immunoglobulin E-set
Similarity search - Domain/homology
COPPER (II) ION / COPPER (I) ION / Carbohydrate binding module family 33 and 10 domain protein
Similarity search - Component
Biological speciesTeredinibacter turnerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsFowler, C.A. / Sabbadin, F. / Ciano, L. / Hemsworth, G.R. / Elias, L. / Bruce, N.C. / McQueen-Mason, S. / Walton, P. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L001926/1 United Kingdom
CitationJournal: Biotechnol Biofuels / Year: 2019
Title: Discovery, activity and characterisation of an AA10 lytic polysaccharide oxygenase from the shipworm symbiontTeredinibacter turnerae.
Authors: Fowler, C.A. / Sabbadin, F. / Ciano, L. / Hemsworth, G.R. / Elias, L. / Bruce, N. / McQueen-Mason, S. / Davies, G.J. / Walton, P.H.
History
DepositionJun 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate binding module family 33 and 10 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1744
Polymers24,0241
Non-polymers1503
Water3,909217
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, SEC-MALLS used to confirm monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-30 kcal/mol
Surface area8950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.644, 62.516, 43.185
Angle α, β, γ (deg.)90.000, 99.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbohydrate binding module family 33 and 10 domain protein


Mass: 24023.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Teredinibacter turnerae (strain ATCC 39867 / T7901) (bacteria)
Strain: ATCC 39867 / T7901 / Gene: TERTU_0046 / Production host: Escherichia coli (E. coli) / References: UniProt: C5BKQ9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M magnesium formate dehydrate pH 7.0 and 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→36.18 Å / Num. all: 147995 / Num. obs: 37737 / % possible obs: 99.5 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.041 / Rrim(I) all: 0.083 / Net I/σ(I): 12.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4927 / CC1/2: 0.606 / Rpim(I) all: 0.548 / Rrim(I) all: 0.972 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→35.25 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.058
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1751 1841 4.9 %RANDOM
Rwork0.1525 ---
obs0.1537 35875 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 42.45 Å2 / Biso mean: 12.773 Å2 / Biso min: 8.28 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å2-0.27 Å2
2--0.12 Å20 Å2
3---0.97 Å2
Refinement stepCycle: final / Resolution: 1.4→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 3 217 1877
Biso mean--15.29 24.52 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131773
X-RAY DIFFRACTIONr_bond_other_d0.0370.0181409
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.6442437
X-RAY DIFFRACTIONr_angle_other_deg2.4431.5713306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3495222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89723.364110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10515238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.853158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022091
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02413
X-RAY DIFFRACTIONr_mcbond_it0.8411.238850
X-RAY DIFFRACTIONr_mcbond_other0.8291.235849
X-RAY DIFFRACTIONr_mcangle_it1.2921.8571066
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 142 -
Rwork0.29 2552 -
all-2694 -
obs--96.52 %

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