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Basic information

Entry
Database: PDB / ID: 4eis
TitleStructural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases (PMO-3)
Components(polysaccharide monooxygenase- ...) x 2
KeywordsOXIDOREDUCTASE / GH61 / PMO / cellulase / biofuels / CBM33 / copper monooxygenase / peroxide / superoxide / cbp21 / beta-sandwich fold / Secreted
Function / homology
Function and homology information


extracellular region / metal ion binding
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
COPPER (II) ION / PEROXIDE ION / Endoglucanase IV
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsLi, X. / Beeson, W.T. / Phillips, C.M. / Marletta, M.A. / Cate, J.H.
CitationJournal: Structure / Year: 2012
Title: Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases.
Authors: Li, X. / Beeson, W.T. / Phillips, C.M. / Marletta, M.A. / Cate, J.H.
History
DepositionApr 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: polysaccharide monooxygenase-3
B: polysaccharide monooxygenase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5547
Polymers48,5462
Non-polymers1,0085
Water13,709761
1
A: polysaccharide monooxygenase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8014
Polymers24,2811
Non-polymers5203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: polysaccharide monooxygenase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7533
Polymers24,2651
Non-polymers4882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.740, 77.890, 82.050
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Polysaccharide monooxygenase- ... , 2 types, 2 molecules AB

#1: Protein polysaccharide monooxygenase-3


Mass: 24281.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PMO-3 (NCU07898) was purified from Neurospora crassa secretome
Source: (natural) Neurospora crassa (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
References: UniProt: Q7SA19
#2: Protein polysaccharide monooxygenase-3


Mass: 24265.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PMO-3 (NCU07898) was purified from Neurospora crassa secretome
Source: (natural) Neurospora crassa (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
References: UniProt: Q7SA19

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Sugars , 1 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 764 molecules

#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-PER / PEROXIDE ION / Peroxide


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 761 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 8.5 / Details: pH 8.5, SMALL TUBES, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.592
11-h,-k,l20.408
ReflectionResolution: 1.37→35.74 Å / Num. obs: 89009

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→35.74 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.87 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.011 / ESU R Free: 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1492 4655 5.2 %RANDOM
Rwork0.1158 ---
obs0.1176 88930 94.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.19 Å2 / Biso mean: 14.7298 Å2 / Biso min: 5.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å24.53 Å2
2---0.65 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.37→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 60 761 4246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023608
X-RAY DIFFRACTIONr_bond_other_d0.0020.023305
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9714956
X-RAY DIFFRACTIONr_angle_other_deg0.8123.0037467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6925448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.09223.597139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.74815467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9841512
X-RAY DIFFRACTIONr_chiral_restr0.0780.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02812
X-RAY DIFFRACTIONr_rigid_bond_restr1.72136913
X-RAY DIFFRACTIONr_sphericity_free22.3755765
X-RAY DIFFRACTIONr_sphericity_bonded9.59956786
LS refinement shellResolution: 1.37→1.405 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 323 -
Rwork0.246 5976 -
all-6299 -
obs--90.7 %

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