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

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Basic information

Entry
Database: PDB / ID: 3tbb
TitleSmall laccase from Streptomyces viridosporus T7A; alternate crystal form.
Componentssmall laccase, oxidoreductase
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, 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 / OXYGEN MOLECULE / PHOSPHATE ION / 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 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 1.4Sep 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_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, oxidoreductase
B: small laccase, oxidoreductase
C: small laccase, oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,16225
Polymers102,6393
Non-polymers1,52322
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-196 kcal/mol
Surface area27830 Å2
MethodPISA
2
A: small laccase, oxidoreductase
B: small laccase, oxidoreductase
C: small laccase, oxidoreductase
hetero molecules

A: small laccase, oxidoreductase
B: small laccase, oxidoreductase
C: small laccase, oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,32550
Polymers205,2786
Non-polymers3,04744
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area31480 Å2
ΔGint-421 kcal/mol
Surface area51860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.000, 127.000, 155.070
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsDetermined via gel-filtration chromatography.

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Components

#1: Protein small laccase, oxidoreductase


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-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: J9PBR2*PLUS, laccase
#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.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Protein concentrationw as 20 mg/ml in Tris-HCl (pH 7.9); the precipitant contained 5% 2-propanol, and 2.5 M dibasic potassium phosphate/monobasic sodium phosphate (pH 5.5)., VAPOR DIFFUSION, ...Details: Protein concentrationw as 20 mg/ml in Tris-HCl (pH 7.9); the precipitant contained 5% 2-propanol, and 2.5 M dibasic potassium phosphate/monobasic sodium phosphate (pH 5.5)., 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: 2.3→30 Å / Num. all: 64712 / Num. obs: 64657 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.195 Å2 / Rmerge(I) obs: 0.214 / Net I/σ(I): 15.12
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.3-2.380.0172.239230462191100
2.38-2.480.0172.559986267011100
2.48-2.590.0173.319337162631100
2.59-2.730.0174.479705165121100
2.73-2.90.0176.429510263801100
2.9-3.120.0179.839419463231100
3.12-3.430.01715.89548064201100
3.43-3.930.01724.749675665461100
3.93-4.930.01736.849493364581100
4.93-300.01742.78962506835199.3

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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: 3TAS

3tas


Resolution: 2.3→29.931 Å / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.8789 / SU ML: 0.59 / σ(F): 1.99 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 3232 5 %random
Rwork0.161 ---
all0.182 64712 --
obs0.1632 64597 99.96 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.296 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 84.17 Å2 / Biso mean: 32.367 Å2 / Biso min: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.0349 Å2-0 Å20 Å2
2--0.0349 Å2-0 Å2
3----0.0699 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6421 0 53 563 7037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086672
X-RAY DIFFRACTIONf_angle_d1.3429061
X-RAY DIFFRACTIONf_chiral_restr0.112926
X-RAY DIFFRACTIONf_plane_restr0.0081198
X-RAY DIFFRACTIONf_dihedral_angle_d13.1462386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.33440.2561390.234726332772100
2.3344-2.37090.27491370.228526182755100
2.3709-2.40970.30331400.232426452785100
2.4097-2.45120.291390.240926542793100
2.4512-2.49580.29521390.233326312770100
2.4958-2.54380.25621400.214626502790100
2.5438-2.59570.23261380.193826362774100
2.5957-2.65210.24441390.193726342773100
2.6521-2.71370.24231400.182826602800100
2.7137-2.78150.23911390.186126482787100
2.7815-2.85670.24761400.178426492789100
2.8567-2.94070.22891400.170626612801100
2.9407-3.03550.18771400.160326582798100
3.0355-3.14390.19591390.150826352774100
3.1439-3.26960.17141410.152726792820100
3.2696-3.41820.20251400.145426602800100
3.4182-3.59820.20161400.145826652805100
3.5982-3.82320.22151410.147926722813100
3.8232-4.11770.1721420.131326902832100
4.1177-4.53080.14931430.113227142857100
4.5308-5.18350.17261410.112826922833100
5.1835-6.51950.15641440.139427472891100
6.5195-29.93330.21551510.20272834298599

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