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- PDB-5wsz: Crystal structure of a lytic polysaccharide monooxygenase,BtLPMO1... -

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Basic information

Entry
Database: PDB / ID: 5wsz
TitleCrystal structure of a lytic polysaccharide monooxygenase,BtLPMO10A, from Bacillus thuringiensis
ComponentsLpmO10A
KeywordsOXIDOREDUCTASE / copper-dependent / monooxygenase / AA10
Function / homology
Function and homology information


transferase activity / metal ion binding
Similarity search - Function
chitin-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
Similarity search - Domain/homology
COPPER (II) ION / LpmO10A / Acetyltransferase domain protein
Similarity search - Component
Biological speciesBacillus thuringiensis subsp. kurstaki (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.565 Å
AuthorsZhao, Y. / Zhang, H. / Yin, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31300668 China
CitationJournal: To Be Published
Title: Crystal structure of a lytic polysaccharide monooxygenase,BtLPMO10A, from Bacillus thuringiensis
Authors: Zhao, Y. / Zhang, H. / Yin, H.
History
DepositionDec 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LpmO10A
B: LpmO10A
C: LpmO10A
D: LpmO10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7458
Polymers74,4914
Non-polymers2544
Water2,342130
1
A: LpmO10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6862
Polymers18,6231
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area7280 Å2
MethodPISA
2
B: LpmO10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6862
Polymers18,6231
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area7230 Å2
MethodPISA
3
C: LpmO10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6862
Polymers18,6231
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area7140 Å2
MethodPISA
4
D: LpmO10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6862
Polymers18,6231
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.021, 73.446, 113.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
LpmO10A


Mass: 18622.801 Da / Num. of mol.: 4 / Fragment: UNP residues 35-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis subsp. kurstaki (bacteria)
Gene: lpmO10A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0C5K362, UniProt: A0A0F6FRT6*PLUS
#2: Chemical
ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 20252 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.072 / Net I/σ(I): 10.9
Reflection shellResolution: 2.57→2.66 Å / Rmerge(I) obs: 0.784 / Rpim(I) all: 0.31 / % possible all: 91.06

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
PHENIXphasing
HKL-3000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BEM

2bem


Resolution: 2.565→47.118 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 896 4.87 %RANDOM
Rwork0.2035 ---
obs0.2058 18385 91.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.565→47.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 4 130 5378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035404
X-RAY DIFFRACTIONf_angle_d0.8417375
X-RAY DIFFRACTIONf_dihedral_angle_d12.6481923
X-RAY DIFFRACTIONf_chiral_restr0.035785
X-RAY DIFFRACTIONf_plane_restr0.006962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5649-2.72560.3801890.28092017X-RAY DIFFRACTION63
2.7256-2.9360.32871270.26872676X-RAY DIFFRACTION85
2.936-3.23140.33241640.24863109X-RAY DIFFRACTION99
3.2314-3.69890.24631580.21413178X-RAY DIFFRACTION100
3.6989-4.65950.22341890.17393186X-RAY DIFFRACTION100
4.6595-47.12550.20381690.17223323X-RAY DIFFRACTION99

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