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Basic information

Entry
Database: PDB / ID: 4eir
TitleStructural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenases (PMO-2)
Componentspolysaccharide monooxygenase-2
KeywordsOXIDOREDUCTASE / GH61 / polysaccharide monooxygenase / 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 / OXYGEN MOLECULE / Endoglucanase II
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / 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_ref_seq_dif / 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_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.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
Revision 1.3Sep 13, 2023Group: 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: polysaccharide monooxygenase-2
B: polysaccharide monooxygenase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,41010
Polymers46,5922
Non-polymers8188
Water9,656536
1
A: polysaccharide monooxygenase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7055
Polymers23,2961
Non-polymers4094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: polysaccharide monooxygenase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7055
Polymers23,2961
Non-polymers4094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-33 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.170, 41.990, 69.250
Angle α, β, γ (deg.)90.00, 97.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein polysaccharide monooxygenase-2


Mass: 23296.123 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: PMO-2 (NCU01050) 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: Q1K8B6
#4: 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.: 2
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

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Non-polymers , 4 types, 542 molecules

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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.1→22.86 Å / Num. obs: 155130

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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
Starting model: PDB ENTRY 3EJA

3eja


Resolution: 1.1→22.86 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.592 / SU ML: 0.012 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.006 / ESU R Free: 0.006 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
RfactorNum. reflection% reflectionSelection details
Rfree0.149 7547 5 %RANDOM
Rwork0.132 ---
obs0.133 149934 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.55 Å2
Baniso -1Baniso -2Baniso -3
1-6.87 Å20 Å2-0.73 Å2
2---3.44 Å2-0 Å2
3----3.43 Å2
Refinement stepCycle: LAST / Resolution: 1.1→22.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 46 536 3854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023467
X-RAY DIFFRACTIONr_bond_other_d0.0040.022249
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9624746
X-RAY DIFFRACTIONr_angle_other_deg1.0583.0035512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2865460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90424.758124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.37415498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4181510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02666
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr1.29135716
X-RAY DIFFRACTIONr_sphericity_free25.8035154
X-RAY DIFFRACTIONr_sphericity_bonded13.40956006
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 549 -
Rwork0.323 10069 -
obs--93.62 %

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