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- PDB-3tbc: Small laccase from Streptomyces viridosporus T7A; alternate cryst... -

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Basic information

Entry
Database: PDB / ID: 3tbc
TitleSmall laccase from Streptomyces viridosporus T7A; alternate crystal form complexed with acetovanillone.
Componentssmall laccase, two-domain laccase, multi-copper oxidase
KeywordsOXIDOREDUCTASE / two-domain laccase / acitovanillone / none / 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, 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 / 1-(4-hydroxy-3-methoxyphenyl)ethanone / OXYGEN MOLECULE / PHOSPHATE ION / Small laccase, multi-copper oxidase
Similarity search - Component
Biological speciesStreptomyces viridosporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 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 5, 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 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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, two-domain laccase, multi-copper oxidase
B: small laccase, two-domain laccase, multi-copper oxidase
C: small laccase, two-domain laccase, multi-copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,46026
Polymers102,6393
Non-polymers1,82123
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-200 kcal/mol
Surface area28050 Å2
MethodPISA
2
A: small laccase, two-domain laccase, multi-copper oxidase
B: small laccase, two-domain laccase, multi-copper oxidase
C: small laccase, two-domain laccase, multi-copper oxidase
hetero molecules

A: small laccase, two-domain laccase, multi-copper oxidase
B: small laccase, two-domain laccase, multi-copper oxidase
C: small laccase, two-domain laccase, multi-copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,91952
Polymers205,2786
Non-polymers3,64146
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area33100 Å2
ΔGint-416 kcal/mol
Surface area51140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.020, 127.020, 155.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-447-

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, two-domain laccase, multi-copper oxidase


Mass: 34212.988 Da / Num. of mol.: 3 / Fragment: copper oxidase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridosporus (bacteria) / Strain: T7A / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: J9PBR2*PLUS, laccase

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Non-polymers , 6 types, 336 molecules

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


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


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-I75 / 1-(4-hydroxy-3-methoxyphenyl)ethanone


Mass: 166.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O3
#6: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein concentration was 20 mg/mL in 20 mM Tris-HCl, the precipitant contained 5% 2-propanol, and 2.5 M dibasic potassium phosphate/monobasic sodium phosphate (pH 5.5). The crystals were ...Details: Protein concentration was 20 mg/mL in 20 mM Tris-HCl, the precipitant contained 5% 2-propanol, and 2.5 M dibasic potassium phosphate/monobasic sodium phosphate (pH 5.5). The crystals were soaked overnight in mother liqueur containing 20 mM acetovanillone, 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: Dec 20, 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: 2.7→20 Å / Num. all: 40419 / Num. obs: 40270 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.312 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 15.42
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.7-2.770.9742.2256432927199.9
2.77-2.850.7872.772579628911100
2.85-2.930.6243.51254642819199.9
2.93-3.020.5264.222454026821100
3.02-3.120.3765.81242252635199.9
3.12-3.230.3186.942348525401100
3.23-3.350.2528.472326125111100
3.35-3.490.18411.482195823651100
3.49-3.640.14813.962124922941100
3.64-3.820.12516.272014621781100
3.82-4.020.09819.651930220921100
4.02-4.270.0823.83179591959199.9
4.27-4.560.06628.771716418791100
4.56-4.930.06429.131578517341100
4.93-5.40.05732.361456916051100
5.4-6.040.05732.421325814621100
6.04-6.970.05233.631176413111100
6.97-8.540.04436.99979811031100
8.54-12.070.03147.376208901100
12.07-200.03445.662918393174.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_764refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing
RefinementResolution: 2.7→19.757 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.856 / SU ML: 0.63 / σ(F): 1.99 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 2013 5 %
Rwork0.1569 38213 -
obs0.1595 40226 99.95 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.289 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 162.69 Å2 / Biso mean: 46.6641 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.958 Å20 Å20 Å2
2---0.958 Å2-0 Å2
3---1.916 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6421 0 74 313 6808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086668
X-RAY DIFFRACTIONf_angle_d1.2759053
X-RAY DIFFRACTIONf_chiral_restr0.102924
X-RAY DIFFRACTIONf_plane_restr0.0071195
X-RAY DIFFRACTIONf_dihedral_angle_d13.7122374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7001-2.76750.3211410.278126782819
2.7675-2.84210.27261420.24526992841
2.8421-2.92550.33411410.216926792820
2.9255-3.01960.29091440.224527312875
3.0196-3.12710.26451420.205526982840
3.1271-3.25180.2811430.194127022845
3.2518-3.39910.25281420.168527092851
3.3991-3.57730.18841420.150426942836
3.5773-3.79990.21341440.13927252869
3.7999-4.09090.19651450.130727632908
4.0909-4.49820.13321430.09827092852
4.4982-5.13910.15161450.107327712916
5.1391-6.43730.17351460.126227752921
6.4373-19.75760.19281530.176228803033
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)
11.6825-0.0655-0.0922.5990.61372.9109-0.0583-0.0984-0.27160.6171-0.1475-0.09930.86120.02890.10030.4229-0.0287-0.03230.16010.09650.25664.9612-36.075956.7706
21.7967-0.11420.17962.21711.41122.04270.0183-0.5423-0.74060.1980.2179-0.26240.4089-0.16270.06360.4128-0.04330.00250.2910.09950.278161.5757-35.905858.5632
32.0769-0.6853-0.7732.28320.29632.2022-0.0141-0.156-0.14950.0614-0.19140.30670.0767-0.17240.11220.3439-0.07720.07950.166-0.01170.255552.929-28.362857.3272
40.8091-0.0085-0.14241.32460.3282.91190.13730.0022-0.00930.1617-0.10470.1640.1648-0.19530.01180.2913-0.06650.03120.19580.00980.25856.7574-29.6950.6684
53.6805-0.1598-0.47312.68961.66625.26960.166-0.25760.04720.356-0.1442-0.2759-0.05340.5683-0.08110.2898-0.048-0.02870.34950.04150.327974.9991-21.089457.2831
61.5505-0.51390.21821.68551.16141.876-0.00490.0717-0.02280.02490.0864-0.25260.13940.1483-0.10560.26480.01920.00470.25030.010.203476.3661-23.570743.4945
71.9133-2.05450.40614.57510.27391.5222-0.2014-0.72820.16920.11230.9221-0.67020.18660.9365-0.09320.16150.1418-0.05430.337-0.06520.277786.3819-20.840652.3715
80.53120.45860.17531.05451.49482.53090.03830.38020.1977-0.42170.2606-0.7236-0.57570.5708-0.20150.35770.01190.22750.5064-0.01140.412492.1043-7.206829.3527
91.0863-0.46190.6932.87611.52092.2894-0.12670.29410.0534-0.34560.2536-0.5708-0.19660.6473-0.16530.3107-0.05720.12490.4778-0.04650.423793.8719-7.794131.076
100.9882-0.0004-0.03341.83580.46571.71380.16280.1573-0.09790.00370.1028-0.46670.20420.3629-0.22410.26480.08360.03930.3624-0.06260.353890.6321-16.86539.027
110.7194-0.46620.43541.58291.08872.02850.05590.13910.0363-0.2635-0.0127-0.1985-0.10610.0542-0.09570.2268-0.03490.07580.2513-0.03060.272381.3954-3.924434.7964
120.8682-0.05930.49341.2093-0.11411.54040.07290.1056-0.0398-0.2917-0.0313-0.032-0.06470.1736-0.08120.28160.06440.00680.27220.01820.224369.8308-7.771427.1242
132.05910.4078-1.82280.1252-0.24474.90240.06710.23660.52-0.75280.0412-0.0515-0.65370.0149-0.02010.72240.02930.01420.26360.09840.366968.02285.638425.4059
141.21590.62440.14952.48460.82251.88020.25760.15960.3565-0.4838-0.01990.9284-0.355-0.54080.23510.31120.1441-0.29890.4505-0.10770.353343.298-4.970325.2927
150.7885-0.1555-0.80131.63160.73882.30880.00650.49780.0646-0.4757-0.19710.6997-0.054-0.32980.14820.53140.1562-0.17210.3956-0.070.478643.7814-3.265923.9766
161.8522-1.01350.69173.54020.12840.3013-0.05380.33260.394-0.5996-0.24930.3721-0.7096-0.2967-0.04790.62490.1945-0.17230.20390.00040.373553.16663.474324.7418
172.5178-1.1444-0.26232.37690.40112.10990.0150.24870.4136-0.5395-0.21610.0478-0.3503-0.22980.10120.50810.0646-0.10760.36740.09680.27756.08270.785419.1192
181.0676-0.18140.13221.71140.44761.27150.01350.0542-0.0027-0.3579-0.10370.0958-0.1142-0.12750.13110.36190.0417-0.06690.28050.00170.223754.1394-7.287727.978
191.8427-0.2593-0.16754.41731.90373.8899-0.0116-0.4122-0.0215-0.2727-0.27960.2450.0624-0.50090.18990.2575-0.024-0.0470.342-0.02830.2846.7775-8.426143.1367
201.21630.3787-0.16512.25950.27971.7263-0.0118-0.0906-0.0159-0.1526-0.0720.20910.1708-0.21460.08880.2743-0.0014-0.03810.2556-0.01930.231753.2002-20.070538.9494
214.59751.22042.31734.42252.47783.72380.3734-0.0563-0.18070.9857-0.32350.33050.775-0.7102-0.03860.3544-0.08640.07850.38690.00110.32544.6479-18.944649.2278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:31)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 32:58)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 59:77)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 78:153)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 154:175)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 176:253)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 254:279)A0
8X-RAY DIFFRACTION8chain 'B' and (resseq 2:31)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 32:58)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 59:121)B0
11X-RAY DIFFRACTION11chain 'B' and (resseq 122:175)B0
12X-RAY DIFFRACTION12chain 'B' and (resseq 176:253)B0
13X-RAY DIFFRACTION13chain 'B' and (resseq 254:279)B0
14X-RAY DIFFRACTION14chain 'C' and (resseq 3:31)C0
15X-RAY DIFFRACTION15chain 'C' and (resseq 32:58)C0
16X-RAY DIFFRACTION16chain 'C' and (resseq 59:77)C0
17X-RAY DIFFRACTION17chain 'C' and (resseq 78:107)C0
18X-RAY DIFFRACTION18chain 'C' and (resseq 108:153)C0
19X-RAY DIFFRACTION19chain 'C' and (resseq 154:174)C0
20X-RAY DIFFRACTION20chain 'C' and (resseq 175:253)C0
21X-RAY DIFFRACTION21chain 'C' and (resseq 254:279)C0

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