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- PDB-4oy8: Structure of ScLPMO10B in complex with zinc. -

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Basic information

Entry
Database: PDB / ID: 4oy8
TitleStructure of ScLPMO10B in complex with zinc.
ComponentsPutative secreted cellulose-binding protein
KeywordsOXIDOREDUCTASE / LPMO / AA10 / CBM33 / PMO / GH61 / cellulose degradation / copper monooxygenase
Function / homology
Function and homology information


chitin-binding protein cbp21 / : / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Secreted cellulose-binding protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsForsberg, Z. / Mackenzie, A.K. / Sorlie, M. / Rohr, A.K. / Helland, R. / Arvai, A.S. / Vaaje-Kolstad, G. / Eijsink, V.G.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural and functional characterization of a conserved pair of bacterial cellulose-oxidizing lytic polysaccharide monooxygenases.
Authors: Forsberg, Z. / Mackenzie, A.K. / Srlie, M. / Rhr, A.K. / Helland, R. / Arvai, A.S. / Vaaje-Kolstad, G. / Eijsink, V.G.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_keywords / symmetry
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 1.4Dec 27, 2023Group: 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_struct_conn_angle / refine_hist / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _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_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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative secreted cellulose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,45212
Polymers20,7511
Non-polymers70011
Water4,702261
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.620, 67.620, 107.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-301-

ZN

21A-302-

ZN

31A-309-

ACT

41A-309-

ACT

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Components

#1: Protein Putative secreted cellulose-binding protein / ScLPMO10B


Mass: 20751.391 Da / Num. of mol.: 1 / Fragment: UNP residues 43-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO0643 / Plasmid: pRSET B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RJC1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M zinc acetate, 0.1 M sodium cacodylate, 9 % v/v 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.28 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.4→35 Å / Num. obs: 54273 / % possible obs: 96 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 13.6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.6 / % possible all: 76.7

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementResolution: 1.4→35.79 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.897 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14333 2732 5 %RANDOM
Rwork0.12499 ---
obs0.12588 51493 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.546 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.13 Å2-0 Å2
2--0.13 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.4→35.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 20 261 1745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021529
X-RAY DIFFRACTIONr_bond_other_d0.0010.021287
X-RAY DIFFRACTIONr_angle_refined_deg1.41.92092
X-RAY DIFFRACTIONr_angle_other_deg0.8193.0032949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76224.76284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91315204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.669157
X-RAY DIFFRACTIONr_chiral_restr0.1010.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8930.924748
X-RAY DIFFRACTIONr_mcbond_other0.8961.888744
X-RAY DIFFRACTIONr_mcangle_it1.1371.396930
X-RAY DIFFRACTIONr_mcangle_other1.1371.512931
X-RAY DIFFRACTIONr_scbond_it1.6981.117781
X-RAY DIFFRACTIONr_scbond_other1.6971.117782
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.11.6131162
X-RAY DIFFRACTIONr_long_range_B_refined2.7962091
X-RAY DIFFRACTIONr_long_range_B_other1.9411940
X-RAY DIFFRACTIONr_rigid_bond_restr3.67531520
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded7.02651478
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 147 -
Rwork0.211 2699 -
obs--68.94 %

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