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- PDB-5t7k: X-ray crystal structure of AA13 LPMO -

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Basic information

Entry
Database: PDB / ID: 5t7k
TitleX-ray crystal structure of AA13 LPMO
ComponentsAoAA13
KeywordsMETAL BINDING PROTEIN / ENZYME / ASPERGILLUS ORYZAE AA13 LPMO
Function / homology: / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / membrane / metal ion binding / Inactive AA13 family lytic polysaccharide monooxygenase
Function and homology information
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFrandsen, K.E.H. / Poulsen, J.-C.N. / Tovborg, M. / Johansen, K.S. / Lo Leggio, L.
Funding support Denmark, 1items
OrganizationGrant numberCountry
The Danish Council for Strategic Research12-134923 Denmark
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Learning from oligosaccharide soaks of crystals of an AA13 lytic polysaccharide monooxygenase: crystal packing, ligand binding and active-site disorder.
Authors: Frandsen, K.E. / Poulsen, J.C. / Tovborg, M. / Johansen, K.S. / Lo Leggio, L.
History
DepositionSep 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AoAA13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1746
Polymers25,6911
Non-polymers4835
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-57 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.560, 59.080, 71.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AoAA13


Mass: 25691.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Gene: AO090701000246 / Production host: Aspergillus oryzae (mold) / References: UniProt: Q2U8Y3
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 1.88 Å3/Da / Density % sol: 34.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20%(v/v)PEG3000 0.2M Zn-acetate 0.1 M Malate/MES/TRIS pH5.0
PH range: 4.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 47483 / % possible obs: 98.2 % / Redundancy: 7.52 % / Rrim(I) all: 0.082 / Net I/σ(I): 17.81
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 4.66 % / Mean I/σ(I) obs: 3.59 / Rrim(I) all: 0.433 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OPB

4opb


Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.369 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.042 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13484 1627 3.4 %RANDOM
Rwork0.09118 ---
obs0.09266 45856 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.238 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2---0.15 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 18 409 2226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192129
X-RAY DIFFRACTIONr_bond_other_d0.0010.021769
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.9442941
X-RAY DIFFRACTIONr_angle_other_deg0.97334138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5025291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39725.714105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05115310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.968157
X-RAY DIFFRACTIONr_chiral_restr0.130.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212632
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02497
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_it1.8560.6751077
X-RAY DIFFRACTIONr_mcbond_other1.8560.6741076
X-RAY DIFFRACTIONr_mcangle_it2.6311.0261385
X-RAY DIFFRACTIONr_mcangle_other2.631.0261386
X-RAY DIFFRACTIONr_scbond_it3.2370.9411052
X-RAY DIFFRACTIONr_scbond_other3.2370.9411052
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7081.3111553
X-RAY DIFFRACTIONr_long_range_B_refined6.7668.8752971
X-RAY DIFFRACTIONr_long_range_B_other5.0377.2352682
X-RAY DIFFRACTIONr_rigid_bond_restr4.52633898
X-RAY DIFFRACTIONr_sphericity_free44.64577
X-RAY DIFFRACTIONr_sphericity_bonded12.77454172
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 113 -
Rwork0.171 2971 -
obs--87.51 %

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