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- PDB-8r7i: X-ray structure of blue laccase BP76 from the termite Neocapriter... -

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Basic information

Entry
Database: PDB / ID: 8r7i
TitleX-ray structure of blue laccase BP76 from the termite Neocapritermes taracua
ComponentsLaccase BP76
KeywordsOXIDOREDUCTASE / insect / defence / protein stabilisation / glycosylation / allysine
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding
Similarity search - Function
Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal ...Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / HYDROXIDE ION / 1,4-benzoquinone / : / : / Laccase BP76
Similarity search - Component
Biological speciesNeocapritermes taracua (cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSkerlova, J. / Brynda, J. / Rezacova, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Crystal structure of blue laccase BP76, a unique termite suicidal defense weapon.
Authors: Skerlova, J. / Brynda, J. / Sobotnik, J. / Zakopcanik, M. / Novak, P. / Bourguignon, T. / Sillam-Dusses, D. / Rezacova, P.
History
DepositionNov 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Laccase BP76
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,46020
Polymers70,3051
Non-polymers5,15519
Water18,1771009
1
A: Laccase BP76
hetero molecules

A: Laccase BP76
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,92040
Polymers140,6112
Non-polymers10,30938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area19760 Å2
ΔGint-135 kcal/mol
Surface area45570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.500, 163.500, 89.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-900-

HOH

21A-1539-

HOH

31A-1696-

HOH

41A-1765-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Laccase BP76


Mass: 70305.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neocapritermes taracua (cockroach) / References: UniProt: A0A0S3AND7, laccase

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Sugars , 4 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1244.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-1-2/a3-b1_a4-c1_a6-g1_c4-d1_d3-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-3-O-sulfo-alpha-D-mannopyranose-(1-3)-[alpha-D- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-3-O-sulfo-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1194.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp3SO3]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 3-O-sulfo-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2- ...3-O-sulfo-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1283.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp3SO3]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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.: 1
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 , 8 types, 1024 molecules

#6: Chemical ChemComp-YKK / 2-methyl-5-oxidanyl-cyclohexa-2,5-diene-1,4-dione


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PLQ / 1,4-benzoquinone / cyclohexa-2,5-diene-1,4-dione / QUINONE RING OF THE PLASTOQUINONE 9


Mass: 108.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-YMR / 2-methylcyclohexa-2,5-diene-1,4-dione


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#12: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1009 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 4.5 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 100 mM sodium acetate pH 4.5, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.362, 0.918
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.3621
20.9181
ReflectionResolution: 1.8→47.2 Å / Num. obs: 126421 / % possible obs: 99.7 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.143 / Net I/σ(I): 12.12
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.910.821202050.90.8641
1.91-2.040.528190890.9480.5581
2.04-2.20.345177330.9770.3621
2.2-2.410.246164240.9860.2581
2.41-2.70.178148820.9920.1881
2.7-3.110.125131520.9950.1311
3.11-3.810.083112070.9970.0881
3.81-5.360.06387180.9980.0661
5.36-47.20.05350110.9990.0561

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata scaling
SHELXphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→47.2 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.976 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14484 3179 2.5 %RANDOM
Rwork0.13221 ---
obs0.13253 123978 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.842 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å2-0 Å2
2--1.04 Å2-0 Å2
3----3.36 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4897 0 323 1009 6229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0125687
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165120
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.8277802
X-RAY DIFFRACTIONr_angle_other_deg2.8431.74611884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3195689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.381537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89310821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.026626
X-RAY DIFFRACTIONr_gen_planes_other0.0520.021286
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_it2.1942.5472626
X-RAY DIFFRACTIONr_mcbond_other2.1882.5472626
X-RAY DIFFRACTIONr_mcangle_it3.0844.5823313
X-RAY DIFFRACTIONr_mcangle_other3.0834.5853314
X-RAY DIFFRACTIONr_scbond_it3.7373.2343061
X-RAY DIFFRACTIONr_scbond_other3.7363.2353062
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4145.7884474
X-RAY DIFFRACTIONr_long_range_B_refined9.73936.3431594
X-RAY DIFFRACTIONr_long_range_B_other9.7436.3431595
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.844 Å
RfactorNum. reflection% reflection
Rfree0.236 230 -
Rwork0.228 9003 -
obs--98.47 %

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