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- PDB-5iju: Structure of an AA10 Lytic Polysaccharide Monooxygenase from Baci... -

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Entry
Database: PDB / ID: 5iju
TitleStructure of an AA10 Lytic Polysaccharide Monooxygenase from Bacillus amyloliquefaciens with Cu(II) bound
ComponentsBaAA10 Lytic Polysaccharide Monooxygenase
KeywordsOXIDOREDUCTASE / lytic polysaccharide monooxygenase / copper II / CAZy AA10
Function / homologychitin-binding protein cbp21 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta / COPPER (II) ION / :
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsGregory, R.C. / Hemsworth, G.R. / Turkenburg, J.P. / Hart, S.J. / Walton, P.H. / Davies, G.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I014802/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L000423 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L021633/1 United Kingdom
Citation
Journal: Dalton Trans / Year: 2016
Title: Activity, stability and 3-D structure of the Cu(ii) form of a chitin-active lytic polysaccharide monooxygenase from Bacillus amyloliquefaciens.
Authors: Gregory, R.C. / Hemsworth, G.R. / Turkenburg, J.P. / Hart, S.J. / Walton, P.H. / Davies, G.J.
#1: Journal: J. Am. Chem. Soc. / Year: 2013
Title: The copper active site of CBM33 polysaccharide oxygenases.
Authors: Hemsworth, G.R. / Taylor, E.J. / Kim, R.Q. / Gregory, R.C. / Lewis, S.J. / Turkenburg, J.P. / Parkin, A. / Davies, G.J. / Walton, P.H.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BaAA10 Lytic Polysaccharide Monooxygenase
B: BaAA10 Lytic Polysaccharide Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9857
Polymers39,6942
Non-polymers2915
Water5,080282
1
A: BaAA10 Lytic Polysaccharide Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9733
Polymers19,8471
Non-polymers1262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BaAA10 Lytic Polysaccharide Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0134
Polymers19,8471
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.779, 73.482, 75.457
Angle α, β, γ (deg.)90.000, 100.400, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein BaAA10 Lytic Polysaccharide Monooxygenase / RBAM17540


Mass: 19847.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein was produced as a SUMO fusion, the SUMO domain removed using SUMO protease during purification
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: RBAM17540, BAMF_1859 / Plasmid: Champion-pETSUMO / Details (production host): Invitrogen / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: E1UUV3
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.4 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M NaOAc pH 5.0, 20 % PEG-6000, 0.2 M CaCl2 Micro seeded using crystals grown in 0.1 M MMT pH 4.0, 25 % PEG-1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→37.11 Å / Num. obs: 41043 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 7.2 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.142 / Net I/σ(I): 5.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2YOX

2yox


Resolution: 1.7→37.11 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.829 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.128
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 2062 5 %RANDOM
Rwork0.2229 ---
obs0.2249 41020 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 34.94 Å2 / Biso mean: 9.4268 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.42 Å2
2--0.28 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 11 282 3075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192876
X-RAY DIFFRACTIONr_bond_other_d00.022596
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9023912
X-RAY DIFFRACTIONr_angle_other_deg3.76635976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9795354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39724.559136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35815424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.785158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213316
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02708
X-RAY DIFFRACTIONr_mcbond_it0.6640.8451422
X-RAY DIFFRACTIONr_mcbond_other0.6640.8441421
X-RAY DIFFRACTIONr_mcangle_it1.1181.2641774
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 150 -
Rwork0.282 2892 -
all-3042 -
obs--99.25 %

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