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- PDB-6ndq: Crystal structure of a LPMO from Kitasatospora papulosa -

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Basic information

Entry
Database: PDB / ID: 6ndq
TitleCrystal structure of a LPMO from Kitasatospora papulosa
Componentslytic polysaccharide monooxygenase
KeywordsOXIDOREDUCTASE / Lytic polysaccharide monooxygenase
Function / homologychitin-binding protein cbp21 / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta / Chitin-binding domain 3 protein
Function and homology information
Biological species[Kitasatospora] papulosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsCorrea, T.L.C. / Tomazini Jr., A. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)15/26982-0 Brazil
CitationJournal: To Be Published
Title: Crystal structure of a LPMO from Kitasatospora papulosa
Authors: Correa, T.L.C. / Tomazini Jr., A. / Murakami, M.T.
History
DepositionDec 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)43,3252
Polymers43,3252
Non-polymers00
Water3,819212
1
A: lytic polysaccharide monooxygenase


Theoretical massNumber of molelcules
Total (without water)21,6621
Polymers21,6621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: lytic polysaccharide monooxygenase


Theoretical massNumber of molelcules
Total (without water)21,6621
Polymers21,6621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.207, 109.574, 42.775
Angle α, β, γ (deg.)90.00, 113.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein lytic polysaccharide monooxygenase


Mass: 21662.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Kitasatospora] papulosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: E8W3L9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.85 Å3/Da / Density % sol: 33.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT buffer pH 4.0 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.453 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.453 Å / Relative weight: 1
ReflectionResolution: 1.6→39.24 Å / Num. obs: 39856 / % possible obs: 96.3 % / Redundancy: 3.18 % / Net I/σ(I): 8.9
Reflection shellResolution: 1.6→1.7 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OY6

4oy6


Resolution: 1.601→33.088 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.97
RfactorNum. reflection% reflection
Rfree0.237 1950 4.89 %
Rwork0.1963 --
obs0.1982 39847 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→33.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 0 212 3220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073129
X-RAY DIFFRACTIONf_angle_d0.8374287
X-RAY DIFFRACTIONf_dihedral_angle_d4.8992073
X-RAY DIFFRACTIONf_chiral_restr0.055425
X-RAY DIFFRACTIONf_plane_restr0.006570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.601-1.64110.42931220.36682314X-RAY DIFFRACTION83
1.6411-1.68540.4111190.32512601X-RAY DIFFRACTION93
1.6854-1.7350.36671250.32012669X-RAY DIFFRACTION96
1.735-1.7910.30061340.27662713X-RAY DIFFRACTION97
1.791-1.8550.2641790.23572709X-RAY DIFFRACTION98
1.855-1.92930.26921260.22452757X-RAY DIFFRACTION98
1.9293-2.01710.24071480.20022721X-RAY DIFFRACTION98
2.0171-2.12340.23451240.19022782X-RAY DIFFRACTION99
2.1234-2.25640.26421390.19022770X-RAY DIFFRACTION99
2.2564-2.43060.24331850.19522719X-RAY DIFFRACTION99
2.4306-2.67510.22231380.1962823X-RAY DIFFRACTION99
2.6751-3.0620.25741330.20012780X-RAY DIFFRACTION99
3.062-3.85680.2061310.17132755X-RAY DIFFRACTION98
3.8568-33.09550.18151470.15442784X-RAY DIFFRACTION98

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