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- PDB-2xvb: Crystal structure of Laccase from Thermus thermophilus HB27 compl... -

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Basic information

Entry
Database: PDB / ID: 2xvb
TitleCrystal structure of Laccase from Thermus thermophilus HB27 complexed with Hg, crystal of the apoenzyme soaked for 5 min. in 5 mM HgCl2 at 278 K.
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: 1.7 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 25, 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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: LACCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,80323
Polymers48,7911
Non-polymers3,01222
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.456, 110.183, 96.343
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-2069-

HOH

21A-2153-

HOH

31A-2241-

HOH

41A-2244-

HOH

51A-2293-

HOH

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Components

#1: Protein LACCASE


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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE AT THE UNIPROT POSITION 53 IS OCCUPIED BY A LEUCINE BUT THE ELECTRON DENSITY CLEARLY ...THE SEQUENCE AT THE UNIPROT POSITION 53 IS OCCUPIED BY A LEUCINE BUT THE ELECTRON DENSITY CLEARLY SUPPORTS 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: 2.48 Å3/Da / Density % sol: 50.36 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5,70 % MPD. BEFORE DATA COLLECTION THE CRYSTAL WAS SOAKED FOR 5 MINUTES IN 5 MM HGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8321
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 23, 2010
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8321 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 59564 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 15.75 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.14
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.72 / % possible all: 91.4

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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: 1.7→19.689 Å / SU ML: 0.17 / σ(F): 1.91 / Phase error: 15.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1778 2761 5 %
Rwork0.1528 --
obs0.1541 54841 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.572 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 18.986 Å2
Baniso -1Baniso -2Baniso -3
1--0.1301 Å20 Å20 Å2
2--0.5844 Å20 Å2
3----0.4543 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 141 455 4035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194100
X-RAY DIFFRACTIONf_angle_d1.9775658
X-RAY DIFFRACTIONf_dihedral_angle_d19.3931583
X-RAY DIFFRACTIONf_chiral_restr0.109611
X-RAY DIFFRACTIONf_plane_restr0.009748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72930.28491490.22732549X-RAY DIFFRACTION100
1.7293-1.76070.2731230.21072594X-RAY DIFFRACTION100
1.7607-1.79460.22041290.19172588X-RAY DIFFRACTION100
1.7946-1.83120.24441400.18592559X-RAY DIFFRACTION100
1.8312-1.8710.2391410.17882573X-RAY DIFFRACTION100
1.871-1.91450.18411440.17232585X-RAY DIFFRACTION100
1.9145-1.96230.19641470.1622570X-RAY DIFFRACTION100
1.9623-2.01530.18461330.15852576X-RAY DIFFRACTION100
2.0153-2.07460.20011390.15452609X-RAY DIFFRACTION100
2.0746-2.14140.17661510.14342567X-RAY DIFFRACTION100
2.1414-2.21790.18141280.14682585X-RAY DIFFRACTION100
2.2179-2.30650.19181350.14582601X-RAY DIFFRACTION100
2.3065-2.41130.18351300.15092630X-RAY DIFFRACTION100
2.4113-2.53820.17591390.14912563X-RAY DIFFRACTION100
2.5382-2.69690.18531330.14992630X-RAY DIFFRACTION100
2.6969-2.90450.17231330.14412624X-RAY DIFFRACTION100
2.9045-3.19570.16921410.13662614X-RAY DIFFRACTION100
3.1957-3.65550.13911410.12882638X-RAY DIFFRACTION100
3.6555-4.59590.12581200.11912683X-RAY DIFFRACTION100
4.5959-19.69030.16111650.16522742X-RAY DIFFRACTION100

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