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- PDB-4n8u: Two-Domain Laccase from Streptomyces viridochromogenes at 2.4 A r... -

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Basic information

Entry
Database: PDB / ID: 4n8u
TitleTwo-Domain Laccase from Streptomyces viridochromogenes at 2.4 A resolution AC629
ComponentsMulticopper oxidase
KeywordsOXIDOREDUCTASE / TWO-DOMAIN LACCASE / MULTICOPPER BLUE PROTEIN
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence ...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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Multicopper oxidase
Similarity search - Component
Biological speciesStreptomyces viridochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGabdulkhakov, A. / Tischenko, S. / Yurevich, L. / Lisov, A. / Leontievsky, A.
CitationJournal: To be Published
Title: Two-Domain Laccase from Streptomyces viridochromogenes at 2.4 A resolution AC629
Authors: Gabdulkhakov, A. / Tischenko, S. / Yurevich, L. / Lisov, A. / Leontievsky, A.
History
DepositionOct 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: Multicopper oxidase
B: Multicopper oxidase
C: Multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,84819
Polymers91,9413
Non-polymers90716
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-48 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.720, 79.600, 204.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Multicopper oxidase / Laccase


Mass: 30647.119 Da / Num. of mol.: 3 / Fragment: UNP residues 33-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridochromogenes (bacteria)
Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: J9S5G3, laccase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 11% PEG 4000, 0.1M Tris- l, 0.1M NaCl, 1.3% polyacrylic acid 5100 sodium salt, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 25, 2012 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 31995 / Num. obs: 31212 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Biso Wilson estimate: 20.42 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.98
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.63 / Num. unique all: 3607 / % possible all: 87.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TAS

3tas


Resolution: 2.4→42.95 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8889 / SU ML: 0.33 / σ(F): 2.05 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1560 5 %RANDOM
Rwork0.1877 ---
all0.19 31995 --
obs0.1897 31208 97.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.36 Å2 / Biso mean: 20.8567 Å2 / Biso min: 4.79 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6372 0 23 83 6478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016562
X-RAY DIFFRACTIONf_angle_d1.3968916
X-RAY DIFFRACTIONf_chiral_restr0.061928
X-RAY DIFFRACTIONf_plane_restr0.0081181
X-RAY DIFFRACTIONf_dihedral_angle_d15.3562321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.47750.36541220.31492327244986
2.4775-2.5660.32781390.27862630276996
2.566-2.66870.27921400.25042663280398
2.6687-2.79020.2991400.23452658279899
2.7902-2.93720.30211440.246927412885100
2.9372-3.12120.23781430.205727202863100
3.1212-3.36210.23651430.183727182861100
3.3621-3.70030.21351460.16772760290699
3.7003-4.23530.18341440.14632749289399
4.2353-5.33450.15211470.12322782292999
5.3345-42.95640.16661520.14162900305298

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