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- PDB-3tas: Small laccase from Streptomyces viridosporus T7A -

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Basic information

Entry
Database: PDB / ID: 3tas
TitleSmall laccase from Streptomyces viridosporus T7A
ComponentsSmall laccase, multi-copper oxidase
KeywordsOXIDOREDUCTASE / two-domain laccase / secreted
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 / Multicopper oxidase, C-terminal / 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 / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / OXYGEN MOLECULE / Small laccase, multi-copper oxidase
Similarity search - Component
Biological speciesStreptomyces viridosporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 4, 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_asym_id / _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_asym_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_asym_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_asym_id / _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_asym_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_conn.ptnr2_label_seq_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
B: Small laccase, multi-copper oxidase
C: Small laccase, multi-copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,88242
Polymers102,6393
Non-polymers3,24339
Water11,079615
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16220 Å2
ΔGint-361 kcal/mol
Surface area31170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.300, 157.180, 162.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-7-

SO4

21A-398-

HOH

31A-433-

HOH

41A-555-

HOH

DetailsDetermined via gel-filtration chromatography

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Small laccase, multi-copper oxidase


Mass: 34212.988 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridosporus (bacteria) / Strain: T7A / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: J9PBR2*PLUS, laccase

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Non-polymers , 7 types, 654 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O2
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein concentration was 20 mg/mL, containing 50 mM Hepes-K+ (pH 8.0), and 100 mM KCl; the precipitant contained 2.0 M Li2SO4, 5% polyethylene glycol 400, 100 mM MgSO4, 100 mM acetate, ...Details: Protein concentration was 20 mg/mL, containing 50 mM Hepes-K+ (pH 8.0), and 100 mM KCl; the precipitant contained 2.0 M Li2SO4, 5% polyethylene glycol 400, 100 mM MgSO4, 100 mM acetate, VAPOR DIFFUSION, HANGING DROP, temperature 282K

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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: Jul 4, 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: 2.3→20 Å / Num. all: 58365 / Num. obs: 58241 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.668 Å2 / Rmerge(I) obs: 0.221 / Net I/σ(I): 10.51
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.3-2.360.8422.02224994267199.9
2.36-2.420.8262.432734241871100
2.42-2.490.7952.763008140471100
2.49-2.570.7283.323240239241100
2.57-2.660.6233.983174438091100
2.66-2.750.5784.413082136991100
2.75-2.850.4915.32981535631100
2.85-2.970.4146.352879334421100
2.97-3.10.3078.432780133281100
3.1-3.250.24810.322625931401100
3.25-3.430.19412.652517930171100
3.43-3.640.14616.092381228501100
3.64-3.890.12817.912242226971100
3.89-4.20.10520.952047824841100
4.2-4.60.08424.621931923341100
4.6-5.140.07725.451734821101100
5.14-5.940.0824.851535618741100
5.94-7.270.07924.291292315961100
7.27-10.290.06228.19981912541100
10.29-200.05332.854359619184.1

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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: 3CG8

3cg8


Resolution: 2.3→19.692 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8996 / SU ML: 0.51 / σ(F): 1.99 / Phase error: 17.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1929 2911 5 %random
Rwork0.1467 ---
obs0.149 58235 99.98 %-
all-58365 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.805 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 113.71 Å2 / Biso mean: 23.2416 Å2 / Biso min: 2.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.4003 Å2-0 Å20 Å2
2---0.4838 Å2-0 Å2
3---0.0835 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6918 0 148 615 7681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087234
X-RAY DIFFRACTIONf_angle_d1.2699780
X-RAY DIFFRACTIONf_chiral_restr0.1981
X-RAY DIFFRACTIONf_plane_restr0.0071295
X-RAY DIFFRACTIONf_dihedral_angle_d15.3652609
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.33770.26131370.206226212758
2.3377-2.37790.24551380.202326122750
2.3779-2.42110.24871370.193125952732
2.4211-2.46750.25691370.194626072744
2.4675-2.51780.25031360.173925952731
2.5178-2.57240.22071390.177226332772
2.5724-2.63220.21661360.168225902726
2.6322-2.69780.23771390.162426312770
2.6978-2.77060.20221370.164426092746
2.7706-2.85190.23611370.164126032740
2.8519-2.94360.22641380.163126202758
2.9436-3.04850.20251380.159326182756
3.0485-3.170.18581380.144126352773
3.17-3.31370.20851380.142226212759
3.3137-3.48750.18671390.131726372776
3.4875-3.70460.16121380.120826262764
3.7046-3.98850.15061410.116426652806
3.9885-4.38580.15271380.107126402778
4.3858-5.01130.14051420.106926812823
5.0113-6.27960.15691410.127326942835
6.2796-19.6930.18871470.169627912938
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.15530.09330.04570.15380.00510.0832-0.0152-0.00720.0583-0.07620.00930.13470.0047-0.02620.00730.007-0.0115-0.03310.0609-0.02160.1052-27.8957-16.72342.9213
20.11130.0562-0.06410.09810.00830.05180.0201-0.00870.01290.0027-0.0020.05270.00270.00630.00180.0344-0.0074-0.00380.0598-0.0090.0362-11.7818-19.604557.3419
30.1365-0.0508-0.0030.041-0.03550.0586-0.0246-0.0478-0.0476-0.08530.0888-0.024-0.0494-0.06610.00270.1831-0.06460.0150.1192-0.01520.1584-17.5378-13.452170.2056
40.2508-0.0695-0.03730.0846-0.03170.3154-0.0035-0.0239-0.01870.0131-0.0055-0.0440.00270.0285-0.00020.0439-0.0014-0.01150.03980.0010.04039.334-22.204764.0743
50.0774-0.05030.01840.13310.00440.0076-0.0143-0.00640.0261-0.0154-0.0051-0.11270.0202-0.0354-0.00570.05140.010.01410.0542-0.00980.058711.0763-23.633343.4158
60.0522-0.05930.02370.12250.07360.19370.0498-0.09310.03450.07020.0279-0.0090.04120.05570.05370.1504-0.02980.04570.13960.07470.326827.4979-19.789644.7534
70.1647-0.09290.0070.1523-0.05560.1989-0.03210.075-0.0136-0.15820.0163-0.078-0.00310.0132-0.03430.1060.00340.04350.0875-0.01420.053210.9637-22.545323.9145
80.13880.03580.05950.21010.09110.17970.02530.0719-0.0328-0.08720.0123-0.0081-0.0209-0.02980.12870.03660.0047-0.01690.0496-0.0150.0169-9.5519-19.975230.8581
90.02140.0165-0.02850.012-0.02160.0362-0.01510.20950.0109-0.16310.0869-0.0512-0.12050.0076-0.00010.31720.0299-0.07120.1851-0.00950.282-16.5961-13.636618.5332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 33:168)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 169:300)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 301:332)A0
4X-RAY DIFFRACTION4chain 'B' and (resseq 31:205)B0
5X-RAY DIFFRACTION5chain 'B' and (resseq 206:300)B0
6X-RAY DIFFRACTION6chain 'B' and (resseq 301:331)B0
7X-RAY DIFFRACTION7chain 'C' and (resseq 33:168)C0
8X-RAY DIFFRACTION8chain 'C' and (resseq 169:300)C0
9X-RAY DIFFRACTION9chain 'C' and (resseq 301:332)C0

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