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- PDB-5tki: Neurospora crassa polysaccharide monooxygenase 2 resting state jo... -

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Basic information

Entry
Database: PDB / ID: 5tki
TitleNeurospora crassa polysaccharide monooxygenase 2 resting state joint X-ray/neutron refinement
ComponentsLytic polysaccharide monooxygenase
KeywordsOXIDOREDUCTASE / polysaccharide monooxygenase
Function / homology
Function and homology information


cellulose catabolic process / 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 / Related to cel1 protein
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsO'Dell, W.B. / Meilleur, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1069091 United States
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase.
Authors: O'Dell, W.B. / Agarwal, P.K. / Meilleur, F.
History
DepositionOct 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_radiation_wavelength / diffrn_source / entity / pdbx_audit_support / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_audit_support.funding_organization / _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_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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: Lytic polysaccharide monooxygenase
B: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5746
Polymers46,5982
Non-polymers9764
Water6,882382
1
A: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7873
Polymers23,2991
Non-polymers4882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7873
Polymers23,2991
Non-polymers4882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-32 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.120, 42.230, 70.290
Angle α, β, γ (deg.)90.00, 98.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lytic polysaccharide monooxygenase / Related to cel1 protein


Mass: 23299.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: G15G9.090, GE21DRAFT_7469 / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): SuperMan5 / References: UniProt: Q8WZQ2
#2: 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
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6 / Details: PEG 3350, HEPES

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Data collection

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-ID
1298ambient1
2298ambient1
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.542
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D22.85,4.5
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATESep 13, 2016
MAATEL IMAGINE2IMAGE PLATEMar 18, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.5421
22.851
34.51
ReflectionResolution: 1.5→36.1 Å / Num. obs: 58482 / % possible obs: 91.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.04 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Net I/σ(I): 13.8 / Num. measured all: 224095 / Scaling rejects: 61
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.533.80.391022026920.8550.2320.4543.886
8.22-36.13.30.0314144250.9940.0190.03621.498.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.13 Å36.1 Å
Translation5.13 Å36.1 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLM7.2.1data reduction
Aimless0.5.27data scaling
LAUEGEN6data reduction
LSCALE1data scaling
SCALA3.3.22data scaling
PHASER2.6.0phasing
Refinement

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Method to determine structureStarting modelResolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLCross valid methodσ(F)Phase error
MOLECULAR REPLACEMENT4EIR

4eir

1.5-36.097X-RAY DIFFRACTION0.17850.14750.14861967574833.4290.190.13FREE R-VALUE019.15
2.115-32.866NEUTRON DIFFRACTION0.25250.21590.2172630181343.4779.020.3525.08
Refinement stepCycle: LAST / Resolution: 1.5→36.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 58 382 3712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117900
X-RAY DIFFRACTIONf_angle_d1.75313399
X-RAY DIFFRACTIONf_dihedral_angle_d21.281999
X-RAY DIFFRACTIONf_chiral_restr0.076559
X-RAY DIFFRACTIONf_plane_restr0.0141390
NEUTRON DIFFRACTIONf_bond_d0.0117900
NEUTRON DIFFRACTIONf_angle_d1.75313399
NEUTRON DIFFRACTIONf_dihedral_angle_d21.281999
NEUTRON DIFFRACTIONf_chiral_restr0.076559
NEUTRON DIFFRACTIONf_plane_restr0.0141390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.32681190.27183479X-RAY DIFFRACTION80
1.5375-1.57910.21290.21083609X-RAY DIFFRACTION83
1.5791-1.62560.20841340.18473686X-RAY DIFFRACTION84
1.6256-1.6780.21541240.17263751X-RAY DIFFRACTION86
1.678-1.7380.21021360.17453829X-RAY DIFFRACTION88
1.738-1.80760.21351460.17533888X-RAY DIFFRACTION89
1.8076-1.88980.22361430.16913917X-RAY DIFFRACTION90
1.8898-1.98950.19361390.15673997X-RAY DIFFRACTION91
1.9895-2.11410.22911370.15344070X-RAY DIFFRACTION92
2.1141-2.27730.18861500.15754116X-RAY DIFFRACTION94
2.2773-2.50640.18931470.1554182X-RAY DIFFRACTION95
2.5064-2.8690.17551510.15314187X-RAY DIFFRACTION96
2.869-3.61410.19281490.13964315X-RAY DIFFRACTION97
3.6141-36.10720.11181630.10724490X-RAY DIFFRACTION99
2.1155-2.32830.35051350.30943515NEUTRON DIFFRACTION64
2.3283-2.66510.30881370.26364084NEUTRON DIFFRACTION74
2.6651-3.35720.23371680.21954667NEUTRON DIFFRACTION85
3.3572-32.86980.19971900.15515238NEUTRON DIFFRACTION93

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