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- PDB-9cpm: Thermus thermophilus HB27 laccase (Tth-Lac) mutant with partial d... -

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Basic information

Entry
Database: PDB / ID: 9cpm
TitleThermus thermophilus HB27 laccase (Tth-Lac) mutant with partial deletion of beta-hairpin sequence
ComponentsLaccase
KeywordsMETAL BINDING PROTEIN / Extremozyme / High-thermal stability / Beta-hairpin motif / Multicopper oxidase / Trinuclear center (TNC) / Copper coordination
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding
Similarity search - Function
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 / Laccase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLee, J. / Miranda-Zaragoza, B. / Rodriguez-Almazan, C. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Int J Mol Sci / Year: 2025
Title: Structure-Function Relationship of the beta-Hairpin of Thermus thermophilus HB27 Laccase.
Authors: Miranda-Zaragoza, B. / Huerta-Miranda, G.A. / Garcia-Garcia, W.I. / Hernandez-Alvarez, E. / Solano-Peralta, A. / Lee, J. / Strynadka, N. / Miranda-Hernandez, M. / Rodriguez-Almazan, C.
History
DepositionJul 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,76010
Polymers48,0741
Non-polymers6869
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.927, 66.032, 74.057
Angle α, β, γ (deg.)90.00, 100.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Laccase


Mass: 48073.559 Da / Num. of mol.: 1 / Mutation: del M295-H303, A304G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_C1370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72HW2, laccase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES (pH6.5), 12% PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95371 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 11, 2022
RadiationMonochromator: Axilon double crystal/multi-layer monochromator (DCMM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 1.6→66.03 Å / Num. obs: 65047 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.116 / Rrim(I) all: 0.218 / Χ2: 0.62 / Net I/σ(I): 7.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.33 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3216 / CC1/2: 0.464 / Rpim(I) all: 1.515 / Rrim(I) all: 2.789 / Χ2: 0.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALS3.20.0data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→51.17 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.745 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18152 3149 4.8 %RANDOM
Rwork0.15346 ---
obs0.15484 61869 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20.55 Å2
2---0.1 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.6→51.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 29 477 3870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123500
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163401
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.8664752
X-RAY DIFFRACTIONr_angle_other_deg0.6311.7467834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.565429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.901532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33910563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024110
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02788
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_it1.8091.5981716
X-RAY DIFFRACTIONr_mcbond_other1.81.5971715
X-RAY DIFFRACTIONr_mcangle_it2.6312.8632145
X-RAY DIFFRACTIONr_mcangle_other2.6342.8632146
X-RAY DIFFRACTIONr_scbond_it3.3262.031784
X-RAY DIFFRACTIONr_scbond_other3.3262.0321785
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.183.5122608
X-RAY DIFFRACTIONr_long_range_B_refined7.46519.983777
X-RAY DIFFRACTIONr_long_range_B_other7.46619.983778
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 242 -
Rwork0.24 4530 -
obs--99.79 %

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