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- PDB-6ha5: AFGH61B L90V/D131S/M134L/A141W VARIANT -

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Basic information

Entry
Database: PDB / ID: 6ha5
TitleAFGH61B L90V/D131S/M134L/A141W VARIANT
ComponentsEndoglucanase, putative
KeywordsOXIDOREDUCTASE / lytic polysaccharide monooxygenase
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / extracellular region
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 1 - #70 / Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61) / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase B
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsLo Leggio, L. / Poulsen, J.C.N.
CitationJournal: Carbohydr. Res. / Year: 2018
Title: Structure of a lytic polysaccharide monooxygenase from Aspergillus fumigatus and an engineered thermostable variant.
Authors: Lo Leggio, L. / Weihe, C.D. / Poulsen, J.N. / Sweeney, M. / Rasmussen, F. / Lin, J. / De Maria, L. / Wogulis, M.
History
DepositionAug 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 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 / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase, putative
B: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8438
Polymers48,4802
Non-polymers3636
Water6,539363
1
A: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4214
Polymers24,2401
Non-polymers1823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4214
Polymers24,2401
Non-polymers1823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.100, 44.280, 60.000
Angle α, β, γ (deg.)89.640, 108.320, 108.950
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIC / Beg label comp-ID: HIC / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 1 - 228 / Label seq-ID: 1 - 228

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Endoglucanase, putative


Mass: 24239.771 Da / Num. of mol.: 2 / Mutation: L90V/D131S/M134L/A141W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_4G07850 / Production host: Aspergillus oryzae (mold)
References: UniProt: Q4WP32, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 363 / 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: 1.87 Å3/Da / Density % sol: 34.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: reservoir consisting of 0.1 M cobalt chloride, 0.1 M Tris pH 8.5; 20 %w/v Polyvinylpyrrolidone K15 and a 1:1 protein reservoir ratio in 0.3 microliter drop
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03982 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03982 Å / Relative weight: 1
ReflectionResolution: 1.87→20 Å / Num. obs: 27929 / % possible obs: 96.4 % / Redundancy: 3.9 % / Rsym value: 0.063 / Net I/σ(I): 17.8
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 6.4 / Rsym value: 0.25 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZUD

3zud


Resolution: 1.87→19.37 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.049 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.133
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 1404 5 %RANDOM
Rwork0.1389 ---
obs0.1411 26525 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.89 Å2 / Biso mean: 21.613 Å2 / Biso min: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å21 Å20.98 Å2
2---1.38 Å20.37 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 1.87→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 18 366 3798
Biso mean--38.27 30.52 -
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0143612
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173093
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.6614969
X-RAY DIFFRACTIONr_angle_other_deg0.9031.657247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9945479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95425154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10415484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.476154
X-RAY DIFFRACTIONr_chiral_restr0.0650.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02701
X-RAY DIFFRACTIONr_mcbond_it1.7832.0691863
X-RAY DIFFRACTIONr_mcbond_other1.7442.0641858
X-RAY DIFFRACTIONr_mcangle_it2.5133.0912327
Refine LS restraints NCS

Ens-ID: 1 / Number: 7287 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 98 -
Rwork0.182 1959 -
all-2057 -
obs--95.01 %

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