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- PDB-2xu9: Crystal structure of Laccase from Thermus thermophilus HB27 -

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Basic information

Entry
Database: PDB / ID: 2xu9
TitleCrystal structure of Laccase 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 / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / HYDROXIDE ION / Laccase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 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 15, 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: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id ..._pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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
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

Downloads & links

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Assembly

Deposited unit
A: LACCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,95322
Polymers48,7911
Non-polymers2,16221
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.578, 110.339, 96.317
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-2173-

HOH

21A-2178-

HOH

31A-2298-

HOH

41A-2301-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LACCASE /


Mass: 48791.457 Da / Num. of mol.: 1 / Fragment: MATURE FORM, RESIDUES 24-462 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE PRESENCE OF AN ISOLEUCINE AT THE POSITION 53 IS STRONGLY SUPPORTED BY THE ELECTRON DENSITY.
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Plasmid: PET32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q72HW2, laccase

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Non-polymers , 5 types, 570 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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Details

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 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: 2.6 Å3/Da / Density % sol: 52.7 %
Description: PHASES WERE OBTAINED BY THE COMBINATION OF SIGNALS GENERATED BY MR AND SAD AT THE COOPER EDGE
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: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 18, 2009
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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→23 Å / Num. obs: 78986 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 12.48 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.41
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.12 / % possible all: 83.9

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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 1KV7

1kv7


Resolution: 1.501→22.816 Å / SU ML: 0.19 / σ(F): 1.39 / Phase error: 15.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1778 3958 5 %
Rwork0.1534 --
obs0.1546 78896 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.16 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 16.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.1183 Å20 Å20 Å2
2--0.3884 Å20 Å2
3----0.2702 Å2
Refinement stepCycle: LAST / Resolution: 1.501→22.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 133 549 4121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014551
X-RAY DIFFRACTIONf_angle_d1.5146330
X-RAY DIFFRACTIONf_dihedral_angle_d17.0071788
X-RAY DIFFRACTIONf_chiral_restr0.094696
X-RAY DIFFRACTIONf_plane_restr0.009850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5007-1.5190.25691180.24662291X-RAY DIFFRACTION86
1.519-1.53820.28241330.23242525X-RAY DIFFRACTION94
1.5382-1.55850.2311230.21092639X-RAY DIFFRACTION98
1.5585-1.57980.22521430.19482662X-RAY DIFFRACTION99
1.5798-1.60240.18491370.18822657X-RAY DIFFRACTION100
1.6024-1.62630.22391290.18072692X-RAY DIFFRACTION100
1.6263-1.65170.2121420.17522637X-RAY DIFFRACTION100
1.6517-1.67880.21241450.17062673X-RAY DIFFRACTION100
1.6788-1.70770.20141520.16882660X-RAY DIFFRACTION100
1.7077-1.73880.18591300.16362698X-RAY DIFFRACTION100
1.7388-1.77220.19961260.15872721X-RAY DIFFRACTION100
1.7722-1.80830.16761610.14892642X-RAY DIFFRACTION100
1.8083-1.84760.17771290.15122671X-RAY DIFFRACTION100
1.8476-1.89060.18091530.14942667X-RAY DIFFRACTION100
1.8906-1.93790.17991320.14562686X-RAY DIFFRACTION100
1.9379-1.99020.17871550.14332677X-RAY DIFFRACTION100
1.9902-2.04880.17061510.14392690X-RAY DIFFRACTION100
2.0488-2.11480.13781400.13832696X-RAY DIFFRACTION100
2.1148-2.19040.17141630.13942711X-RAY DIFFRACTION100
2.1904-2.2780.15781430.13752665X-RAY DIFFRACTION100
2.278-2.38160.17511280.13912716X-RAY DIFFRACTION100
2.3816-2.5070.17431450.14632716X-RAY DIFFRACTION100
2.507-2.66380.17061470.14492721X-RAY DIFFRACTION100
2.6638-2.86910.1481550.13882701X-RAY DIFFRACTION100
2.8691-3.15720.16081640.13372712X-RAY DIFFRACTION100
3.1572-3.61250.13671280.12752764X-RAY DIFFRACTION100
3.6125-4.54550.13921470.11692762X-RAY DIFFRACTION100
4.5455-22.81820.1741390.16392886X-RAY DIFFRACTION100

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