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- PDB-6rh9: Crystal Structure of Two-Domain Laccase mutant I170F from Strepto... -

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Basic information

Entry
Database: PDB / ID: 6rh9
TitleCrystal Structure of Two-Domain Laccase mutant I170F from Streptomyces griseoflavus
ComponentsTwo-domain laccase
KeywordsOXIDOREDUCTASE / Two-Domain Laccase / laccase / Streptomyces griseoflavus
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / iron ion transport / copper ion binding / plasma membrane
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 / OXYGEN MOLECULE / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V. / Kolyadenko, I.A.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-04-00270a Russian Federation
RAS program "Molecular and Cell Biology and Postgenomic Technologies"
CitationJournal: Int J Mol Sci / Year: 2019
Title: Investigations of Accessibility of T2/T3 Copper Center of Two-Domain Laccase fromStreptomyces griseoflavusAc-993.
Authors: Gabdulkhakov, A. / Kolyadenko, I. / Kostareva, O. / Mikhaylina, A. / Oliveira, P. / Tamagnini, P. / Lisov, A. / Tishchenko, S.
History
DepositionApr 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
G: Two-domain laccase
H: Two-domain laccase
I: Two-domain laccase
J: Two-domain laccase
K: Two-domain laccase
L: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,54170
Polymers417,83612
Non-polymers3,70558
Water8,485471
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,28416
Polymers104,4593
Non-polymers82513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-141 kcal/mol
Surface area27760 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,38017
Polymers104,4593
Non-polymers92114
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-159 kcal/mol
Surface area27220 Å2
MethodPISA
3
G: Two-domain laccase
H: Two-domain laccase
I: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,47019
Polymers104,4593
Non-polymers1,01116
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12260 Å2
ΔGint-137 kcal/mol
Surface area27150 Å2
MethodPISA
4
J: Two-domain laccase
K: Two-domain laccase
L: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,40818
Polymers104,4593
Non-polymers94915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-143 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.250, 94.770, 116.180
Angle α, β, γ (deg.)90.13, 89.95, 92.56
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Two-domain laccase


Mass: 34819.668 Da / Num. of mol.: 12 / Mutation: I170F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4FJ81, laccase

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Non-polymers , 6 types, 529 molecules

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


Mass: 63.546 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25% Smear medium PEG, 0.1 M Bicine, 0.1 M NaCl, 0.05M H3BO3-NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 256815 / % possible obs: 91.4 % / Redundancy: 2.08 % / Rrim(I) all: 0.109 / Net I/σ(I): 10.9
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.8 / Num. unique obs: 12984

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O4Q

5o4q


Resolution: 1.85→47.337 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 28.66
RfactorNum. reflection% reflection
Rfree0.237 12840 5 %
Rwork0.1785 --
obs0.1814 256747 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→47.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25540 0 89 471 26100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826438
X-RAY DIFFRACTIONf_angle_d0.87435905
X-RAY DIFFRACTIONf_dihedral_angle_d20.5749391
X-RAY DIFFRACTIONf_chiral_restr0.0533651
X-RAY DIFFRACTIONf_plane_restr0.0054805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.39292770.35785256X-RAY DIFFRACTION59
1.871-1.8930.36582990.33775699X-RAY DIFFRACTION64
1.893-1.91610.39333250.32856170X-RAY DIFFRACTION70
1.9161-1.94030.38233810.31897234X-RAY DIFFRACTION81
1.9403-1.96590.35664390.30238341X-RAY DIFFRACTION93
1.9659-1.99280.36624430.28248404X-RAY DIFFRACTION95
1.9928-2.02130.33044490.27698544X-RAY DIFFRACTION95
2.0213-2.05140.34974460.26518453X-RAY DIFFRACTION95
2.0514-2.08350.31794450.25218462X-RAY DIFFRACTION95
2.0835-2.11770.30494470.25058487X-RAY DIFFRACTION96
2.1177-2.15420.31124450.24098455X-RAY DIFFRACTION95
2.1542-2.19330.29954460.2388478X-RAY DIFFRACTION95
2.1933-2.23550.32484440.248423X-RAY DIFFRACTION95
2.2355-2.28120.31714460.23248506X-RAY DIFFRACTION95
2.2812-2.33080.28934520.22798569X-RAY DIFFRACTION96
2.3308-2.3850.29714470.20238493X-RAY DIFFRACTION96
2.385-2.44460.26934500.20438551X-RAY DIFFRACTION96
2.4446-2.51070.28464470.20828495X-RAY DIFFRACTION96
2.5107-2.58460.30464510.20888568X-RAY DIFFRACTION95
2.5846-2.6680.29284420.20558388X-RAY DIFFRACTION94
2.668-2.76330.28034370.19658300X-RAY DIFFRACTION93
2.7633-2.8740.26154440.18918435X-RAY DIFFRACTION95
2.874-3.00470.25554400.17038366X-RAY DIFFRACTION95
3.0047-3.16310.24174460.15128463X-RAY DIFFRACTION95
3.1631-3.36130.21174450.15268462X-RAY DIFFRACTION95
3.3613-3.62070.19934380.13988315X-RAY DIFFRACTION94
3.6207-3.98490.18294450.12978450X-RAY DIFFRACTION95
3.9849-4.56110.14884390.11518359X-RAY DIFFRACTION94
4.5611-5.74490.14914340.12438241X-RAY DIFFRACTION93
5.7449-47.3530.18744510.17248540X-RAY DIFFRACTION96

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