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- PDB-2xuw: Crystal Structure of Apolaccase from Thermus thermophilus HB27 -

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Basic information

Entry
Database: PDB / ID: 2xuw
TitleCrystal Structure of Apolaccase from Thermus thermophilus HB27
ComponentsLACCASE
KeywordsOXIDOREDUCTASE / MULTICOPPER OXIDASES
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, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsSerrano-Posada, H. / Valderrama, B. / Rudino-Pinera, E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: X-Ray-Induced Catalytic Active-Site Reduction of a Multicopper Oxidase: Structural Insights Into the Proton-Relay Mechanism and O2-Reduction States.
Authors: Serrano-Posada, H. / Centeno-Leija, S. / Rojas-Trejo, S.P. / Rodriguez-Almazan, C. / Stojanoff, V. / Rudino-Pinera, E.
History
DepositionOct 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: database_PDB_caveat / pdbx_database_status ...database_PDB_caveat / pdbx_database_status / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: LACCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,68217
Polymers48,7911
Non-polymers1,89116
Water9,458525
1
A: LACCASE
hetero molecules

A: LACCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,36434
Polymers97,5832
Non-polymers3,78232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9890 Å2
ΔGint-320 kcal/mol
Surface area33030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.018, 110.125, 96.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2087-

HOH

21A-2139-

HOH

31A-2303-

HOH

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Components

#1: Protein LACCASE / APOLACCASE


Mass: 48791.457 Da / Num. of mol.: 1 / Fragment: MATURE FORM, RESIDUES 24-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Plasmid: PET32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q72HW2, laccase
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 53 TO ILE
Sequence detailsTHE SEQUENCE AT THE UNIPROT DEPOSIT Q4H436 POSITION 53 IS OCCUPIED BY A LEUCINE BUT THE ELECTRON ...THE SEQUENCE AT THE UNIPROT DEPOSIT Q4H436 POSITION 53 IS OCCUPIED BY A LEUCINE BUT THE ELECTRON DENSITY CLEARLY SUPPORT THE PRESENCE OF AN ISOLEUCINE IN THIS POSITION.

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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: 2.47 Å3/Da / Density % sol: 50.13 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 70% MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.3747
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 22, 2010
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSSING.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3747 Å / Relative weight: 1
ReflectionResolution: 1.7→26 Å / Num. obs: 53818 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 16.29 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.75 / % possible all: 82.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XU9

2xu9


Resolution: 1.703→26.472 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 16.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1851 2747 5.1 %
Rwork0.1514 --
obs0.1531 53818 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.01 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 18.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.1269 Å20 Å20 Å2
2--0.4259 Å20 Å2
3----0.5527 Å2
Refinement stepCycle: LAST / Resolution: 1.703→26.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 128 525 4092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154324
X-RAY DIFFRACTIONf_angle_d1.9926010
X-RAY DIFFRACTIONf_dihedral_angle_d18.4541687
X-RAY DIFFRACTIONf_chiral_restr0.151653
X-RAY DIFFRACTIONf_plane_restr0.01813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7027-1.7320.29381150.2512259X-RAY DIFFRACTION88
1.732-1.76350.24571320.20912522X-RAY DIFFRACTION99
1.7635-1.79740.2361560.1852503X-RAY DIFFRACTION99
1.7974-1.83410.20441290.17572520X-RAY DIFFRACTION99
1.8341-1.8740.19781530.17262510X-RAY DIFFRACTION99
1.874-1.91760.23611450.16632519X-RAY DIFFRACTION99
1.9176-1.96550.21651360.16482547X-RAY DIFFRACTION99
1.9655-2.01860.18141320.15162545X-RAY DIFFRACTION100
2.0186-2.0780.21951200.1512573X-RAY DIFFRACTION100
2.078-2.14510.1781350.14632554X-RAY DIFFRACTION100
2.1451-2.22170.19551370.14692563X-RAY DIFFRACTION100
2.2217-2.31060.20081360.13672574X-RAY DIFFRACTION100
2.3106-2.41570.16311280.14432563X-RAY DIFFRACTION100
2.4157-2.5430.18891420.14072584X-RAY DIFFRACTION100
2.543-2.70210.16891340.15082562X-RAY DIFFRACTION100
2.7021-2.91050.18621340.14222605X-RAY DIFFRACTION100
2.9105-3.2030.15841420.132594X-RAY DIFFRACTION100
3.203-3.66540.12351390.12142618X-RAY DIFFRACTION100
3.6654-4.61410.15681510.11112632X-RAY DIFFRACTION100
4.6141-26.47480.18381510.16312724X-RAY DIFFRACTION100

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