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- PDB-4nb7: Crystal Structure of Two-Domain Laccase from Streptomyces LIvidan... -

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Basic information

Entry
Database: PDB / ID: 4nb7
TitleCrystal Structure of Two-Domain Laccase from Streptomyces LIvidans AC1709 in complex with azide after 180 min soaking
ComponentsCopper oxidase
KeywordsOXIDOREDUCTASE / Multicopper blue protein / Two-domain Laccase
Function / homology
Function and homology information


oxidoreductase activity / 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
Chem-7PE / AZIDE ION / COPPER (II) ION / Copper oxidase
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsGabdulkhakov, A. / Tischenko, S. / Yurevich, L. / Lisov, A. / Leontievsky, A.
CitationJournal: To be Published
Title: Crystal Structure of Two-Domain Laccase from Streptomyces Lividans AC1709 in complex with azide after 180 min soaking
Authors: Gabdulkhakov, A. / Tischenko, S. / Yurevich, L. / Lisov, A. / Leontievsky, A.
History
DepositionOct 23, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,28419
Polymers36,9321
Non-polymers2,35218
Water1,58588
1
A: Copper oxidase
hetero molecules

A: Copper oxidase
hetero molecules

A: Copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,85357
Polymers110,7963
Non-polymers7,05754
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area23590 Å2
ΔGint-123 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.510, 177.510, 177.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-578-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Copper oxidase / Laccase


Mass: 36932.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Strain: TK24 / Gene: SSPG_00990 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: D6EFA0, laccase

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Non-polymers , 9 types, 106 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: N3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 6.31 Å3/Da / Density % sol: 80.51 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 31%(v/v) PEG monomethyl ether 550, 0.1M NaCl, 0.1M glycine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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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: Dec 8, 2011 / 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: 2.55→50 Å / Num. obs: 31563 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 58.35 Å2
Reflection shellResolution: 2.55→2.7 Å / % possible all: 96.9

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GYB

4gyb


Resolution: 2.55→44.377 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8788 / SU ML: 0.29 / σ(F): 1.37 / Phase error: 17.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1811 1578 5 %RANDOM
Rwork0.161 ---
all0.163 31734 --
obs0.162 31553 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.72 Å2 / Biso mean: 57.5892 Å2 / Biso min: 40.73 Å2
Refinement stepCycle: LAST / Resolution: 2.55→44.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 146 88 2397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092353
X-RAY DIFFRACTIONf_angle_d1.2373135
X-RAY DIFFRACTIONf_chiral_restr0.046311
X-RAY DIFFRACTIONf_plane_restr0.006400
X-RAY DIFFRACTIONf_dihedral_angle_d17.391893
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 (%)
2.5502-2.63250.29291350.33252552268795
2.6325-2.72660.32941400.285426682808100
2.7266-2.83570.30121410.28126772818100
2.8357-2.96480.26431430.230527092852100
2.9648-3.1210.23941410.20326812822100
3.121-3.31650.2391430.196927162859100
3.3165-3.57250.20331430.164227252868100
3.5725-3.93180.15681440.140227292873100
3.9318-4.50030.12261450.114227592904100
4.5003-5.6680.13081470.110828002947100
5.668-44.38420.16641560.15062959311599

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