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- PDB-9ix9: Mutant H286T Crystal Structure of Two-domain bacterial laccase fr... -

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Basic information

Entry
Database: PDB / ID: 9ix9
TitleMutant H286T Crystal Structure of Two-domain bacterial laccase from the actinobacterium Streptomyces carpinensis VKM Ac-1300
ComponentsTwo-Domain Laccase
KeywordsOXIDOREDUCTASE / Two-Domain Laccase / laccase / Streptomyces carpinensis
Function / homologyCOPPER (II) ION / OXYGEN MOLECULE
Function and homology information
Biological speciesStreptomyces carpinensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V. / Trubitsina, L. / Trubitsin, I. / Leontievsky, A. / Lisov, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mutant H286T Crystal Structure of Two-domain bacterial laccase from the actinobacterium Streptomyces carpinensis VKM Ac-1300
Authors: Gabdulkhakov, A.G. / Tishchenko, T.V. / Trubitsina, L. / Trubitsin, I. / Leontievsky, A. / Lisov, A.
History
DepositionJul 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two-Domain Laccase
B: Two-Domain Laccase
C: Two-Domain Laccase
D: Two-Domain Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,20326
Polymers142,7604
Non-polymers1,44322
Water9,116506
1
A: Two-Domain Laccase
B: Two-Domain Laccase
C: Two-Domain Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,19820
Polymers107,0703
Non-polymers1,12817
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13020 Å2
ΔGint-121 kcal/mol
Surface area28250 Å2
MethodPISA
2
D: Two-Domain Laccase
hetero molecules

D: Two-Domain Laccase
hetero molecules

D: Two-Domain Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,01418
Polymers107,0703
Non-polymers94415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area12910 Å2
ΔGint-122 kcal/mol
Surface area28800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.546, 196.546, 196.546
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11D-644-

HOH

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Components

#1: Protein
Two-Domain Laccase


Mass: 35689.984 Da / Num. of mol.: 4 / Mutation: H286T
Source method: isolated from a genetically manipulated source
Details: VKM Ac-1300 / Source: (gene. exp.) Streptomyces carpinensis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, 25% v/v PEG Smear broad

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54179 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 84750 / % possible obs: 99.9 % / Redundancy: 21.1 % / Biso Wilson estimate: 21.23 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.29 / Net I/σ(I): 8.17
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 2.08 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8403 / CC1/2: 0.91 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→25.81 Å / SU ML: 0.2585 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.2369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2583 3793 5.07 %
Rwork0.2091 70956 -
obs0.2117 74749 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.8 Å2
Refinement stepCycle: LAST / Resolution: 2.05→25.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8493 0 56 506 9055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00678791
X-RAY DIFFRACTIONf_angle_d0.842911928
X-RAY DIFFRACTIONf_chiral_restr0.0581256
X-RAY DIFFRACTIONf_plane_restr0.00851581
X-RAY DIFFRACTIONf_dihedral_angle_d13.74113133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.36571450.28182645X-RAY DIFFRACTION95.58
2.08-2.10.34881340.27162607X-RAY DIFFRACTION95.94
2.1-2.130.35571500.27522563X-RAY DIFFRACTION94.79
2.13-2.160.34821300.2652642X-RAY DIFFRACTION95.42
2.16-2.190.29771100.26932604X-RAY DIFFRACTION94.4
2.19-2.230.38541380.28762561X-RAY DIFFRACTION92.81
2.23-2.270.29041520.25572525X-RAY DIFFRACTION93.08
2.27-2.30.3441210.2612622X-RAY DIFFRACTION93.84
2.3-2.350.33621180.28272536X-RAY DIFFRACTION92.02
2.35-2.390.32271390.26262590X-RAY DIFFRACTION93.33
2.39-2.440.30421290.26982543X-RAY DIFFRACTION93.17
2.44-2.490.30111450.26862597X-RAY DIFFRACTION93.78
2.49-2.550.37111490.26412561X-RAY DIFFRACTION93.45
2.55-2.610.31411400.26242595X-RAY DIFFRACTION93.95
2.62-2.690.351160.25142579X-RAY DIFFRACTION94
2.69-2.760.34561380.26752614X-RAY DIFFRACTION94.12
2.76-2.850.29711490.24582586X-RAY DIFFRACTION93.5
2.85-2.950.29841270.24272593X-RAY DIFFRACTION93.63
2.96-3.070.27211420.22792579X-RAY DIFFRACTION93.51
3.07-3.210.30871450.21352610X-RAY DIFFRACTION94
3.21-3.380.26481260.20592632X-RAY DIFFRACTION95.04
3.38-3.590.20761450.18432715X-RAY DIFFRACTION97.71
3.59-3.870.22721700.16442711X-RAY DIFFRACTION98.06
3.87-4.260.19141710.15342699X-RAY DIFFRACTION98.05
4.26-4.870.16241720.12782761X-RAY DIFFRACTION98.99
4.87-6.120.14091480.13222791X-RAY DIFFRACTION99.42
6.12-25.810.20391440.15542895X-RAY DIFFRACTION99.74

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