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- PDB-3t9w: Small laccase from Amycolatopsis sp. ATCC 39116 -

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Basic information

Entry
Database: PDB / ID: 3t9w
TitleSmall laccase from Amycolatopsis sp. ATCC 39116
Componentssmall laccase, multi-copper oxidase
KeywordsOXIDOREDUCTASE / Two-domain copper oxidase / oxidase / Cu-binding
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 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / NICKEL (II) ION / HYDROGEN PEROXIDE / Small laccase, multi-copper oxidase
Similarity search - Component
Biological speciesAmycolatopsis sp. ATCC 39116 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLukk, T. / Majumdar, S. / Gerlt, J.A. / Nair, S.K.
CitationJournal: Biochemistry / Year: 2014
Title: Roles of small laccases from Streptomyces in lignin degradation.
Authors: Majumdar, S. / Lukk, T. / Solbiati, J.O. / Bauer, S. / Nair, S.K. / Cronan, J.E. / Gerlt, J.A.
History
DepositionAug 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: small laccase, multi-copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5967
Polymers33,2491
Non-polymers3476
Water8,431468
1
A: small laccase, multi-copper oxidase
hetero molecules

A: small laccase, multi-copper oxidase
hetero molecules

A: small laccase, multi-copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,78821
Polymers99,7473
Non-polymers1,04118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11800 Å2
ΔGint-176 kcal/mol
Surface area27500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.180, 110.180, 178.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-376-

HOH

21A-417-

HOH

31A-461-

HOH

41A-749-

HOH

DetailsDetermined via gel-filtration chromatography.

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Components

#1: Protein small laccase, multi-copper oxidase


Mass: 33249.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis sp. ATCC 39116 (bacteria)
Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: J9PBQ8*PLUS, laccase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O

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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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein concentration was 20 mg/mL buffered with 20 mM Tris (pH 7.9), the precipitant contained 3.0 M NaCl and 100 mM Hepes, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 66830 / Num. obs: 66783 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.44 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.46
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.540.812.64439949051100
1.54-1.580.6283.44337647631100
1.58-1.630.5124.174257846431100
1.63-1.680.4125.174182245431100
1.68-1.730.3216.594036343711100
1.73-1.790.2538.353912342231100
1.79-1.860.18711.093795840961100
1.86-1.940.15513.423675239591100
1.94-2.020.11517.533498437681100
2.02-2.120.0921.663377136331100
2.12-2.240.07725.063217734621100
2.24-2.370.06827.93020732481100
2.37-2.540.06330.192845930711100
2.54-2.740.05633.632666928761100
2.74-30.04838.112468326581100
3-3.350.04442.542233524161100
3.35-3.870.04145.121944921111100
3.87-4.740.03946.921654218141100
4.74-6.710.0446.681289014411100
6.71-200.04344.586398782194.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_764refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3CG8

3cg8


Resolution: 1.5→19.657 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8741 / SU ML: 0.37 / σ(F): 2 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 3339 5 %random
Rwork0.1721 ---
obs0.1736 66780 99.99 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.825 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 59.79 Å2 / Biso mean: 22.7589 Å2 / Biso min: 9.64 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 7 468 2582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082266
X-RAY DIFFRACTIONf_angle_d1.3893088
X-RAY DIFFRACTIONf_chiral_restr0.121314
X-RAY DIFFRACTIONf_plane_restr0.011411
X-RAY DIFFRACTIONf_dihedral_angle_d12.673830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.52140.27771370.273626022739
1.5214-1.54410.31881380.251926202758
1.5441-1.56820.24181390.24426312770
1.5682-1.59390.26141380.229126262764
1.5939-1.62140.28841380.231426212759
1.6214-1.65090.25951380.227226212759
1.6509-1.68260.24241370.218325992736
1.6826-1.71690.24081390.209826552794
1.7169-1.75420.2321380.203326172755
1.7542-1.7950.23761380.197426182756
1.795-1.83990.21161390.187826342773
1.8399-1.88960.20941380.183726312769
1.8896-1.94510.19841390.185926362775
1.9451-2.00790.23431380.178826282766
2.0079-2.07950.20481400.173626542794
2.0795-2.16270.17191380.16326282766
2.1627-2.2610.1931390.165326362775
2.261-2.380.20411390.173626432782
2.38-2.52880.20251390.173626442783
2.5288-2.72360.2231410.179426822823
2.7236-2.99690.21161400.180226512791
2.9969-3.42850.21191410.158326902831
3.4285-4.31210.13831420.129926882830
4.3121-19.65890.18621460.154627862932

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