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- PDB-4wtq: Structure of the Ssl1 laccase mutant M295L -

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Basic information

Entry
Database: PDB / ID: 4wtq
TitleStructure of the Ssl1 laccase mutant M295L
ComponentsCopper oxidase
KeywordsOXIDOREDUCTASE / Laccase / multicopper oxidase
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 / Multicopper oxidase, C-terminal / 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 / Multicopper oxidase, C-terminal / 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 ATOM / Copper oxidase
Similarity search - Component
Biological speciesStreptomyces sviceus ATCC 29083 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGunne, M. / Hoeppner, A. / Urlacher, V.B.
CitationJournal: To Be Published
Title: Structure of the Ssl1 laccase mutant M295L
Authors: Gunne, M. / Hoeppner, A. / Urlacher, V.B.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 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: Copper oxidase
B: Copper oxidase
C: Copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,16915
Polymers97,4733
Non-polymers69612
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-118 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.528, 104.795, 164.389
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 Copper oxidase


Mass: 32491.039 Da / Num. of mol.: 3 / Mutation: M295L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sviceus ATCC 29083 (bacteria)
Gene: SSEG_02446 / Production host: Escherichia coli (E. coli) / References: UniProt: B5HSR1, laccase
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM HEPES, pH 7.0, 1.0-1.3 M ammonium sulfate, 5-20 mM hexamminecobalt(III) chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.900002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.900002 Å / Relative weight: 1
ReflectionResolution: 1.8→24.96 Å / Num. obs: 82580 / % possible obs: 99.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M3H

4m3h


Resolution: 1.8→24.58 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.823 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20812 4083 5 %RANDOM
Rwork0.17094 ---
obs0.17277 77770 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.946 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 17 431 6718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196449
X-RAY DIFFRACTIONr_bond_other_d0.0020.025868
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.9228750
X-RAY DIFFRACTIONr_angle_other_deg0.852313463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42422.785316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3115974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5491551
X-RAY DIFFRACTIONr_chiral_restr0.1150.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217466
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021609
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6672.4953229
X-RAY DIFFRACTIONr_mcbond_other2.6622.4943228
X-RAY DIFFRACTIONr_mcangle_it3.7753.7284031
X-RAY DIFFRACTIONr_mcangle_other3.7753.7294032
X-RAY DIFFRACTIONr_scbond_it3.8352.9233220
X-RAY DIFFRACTIONr_scbond_other3.8352.9233220
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9344.1944720
X-RAY DIFFRACTIONr_long_range_B_refined8.82521.2077392
X-RAY DIFFRACTIONr_long_range_B_other8.82421.217393
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 320 -
Rwork0.224 5711 -
obs--99.03 %

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