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- PDB-6h1z: AFGH61B WILD-TYPE -

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Basic information

Entry
Database: PDB / ID: 6h1z
TitleAFGH61B WILD-TYPE
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: 1.57 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
DepositionJul 12, 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
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

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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)48,81510
Polymers48,3692
Non-polymers4458
Water7,566420
1
A: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5077
Polymers24,1851
Non-polymers3236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3073
Polymers24,1851
Non-polymers1232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.670, 43.850, 60.010
Angle α, β, γ (deg.)89.620, 108.330, 109.200
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Endoglucanase, putative


Mass: 24184.715 Da / Num. of mol.: 2
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.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 1.83 Å3/Da / Density % sol: 32.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium thiocyanate pH 6.9, 20 %w/v PEG 3350 (reservoir)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.57→20 Å / Num. obs: 43815 / % possible obs: 91.6 % / Redundancy: 2.5 % / Rsym value: 0.041 / Net I/σ(I): 19.5
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.136 / % possible all: 51.7

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Processing

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

3zud


Resolution: 1.57→19.43 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.393 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.167 2245 5.1 %RANDOM
Rwork0.1285 ---
obs0.1305 41569 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.41 Å2 / Biso mean: 14.517 Å2 / Biso min: 7.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.54 Å20.33 Å2
2---0.72 Å20.26 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.57→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 23 423 3848
Biso mean--29.18 25.95 -
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0143728
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173201
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.6645156
X-RAY DIFFRACTIONr_angle_other_deg1.0651.6537542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0775517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58525.241166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12815525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.84155
X-RAY DIFFRACTIONr_chiral_restr0.0820.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024374
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02712
X-RAY DIFFRACTIONr_mcbond_it1.4091.321907
X-RAY DIFFRACTIONr_mcbond_other1.3661.3181905
X-RAY DIFFRACTIONr_mcangle_it2.011.9742395
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 94 -
Rwork0.188 1702 -
all-1796 -
obs--51.62 %

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