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- PDB-5afa: Crystal structure of Laccase from Thermus thermophilus HB27 compl... -

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Basic information

Entry
Database: PDB / ID: 5afa
TitleCrystal structure of Laccase from Thermus thermophilus HB27 complexed with Ag, crystal of the holoenzyme soaked for 30 m in 5 mM AgNO3 at 278 K.
ComponentsLACCASE
KeywordsOXIDOREDUCTASE / MULTICOPPER OXIDASE
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / outer membrane-bounded periplasmic space / oxidoreductase activity / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / 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, C-terminal / Multicopper oxidase / 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
SILVER ION / COPPER (II) ION / HYDROXIDE ION / Laccase-like protein / Laccase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.193 Å
AuthorsJimenez-Arroyo, N. / Rudino-Pinera, E.
CitationJournal: To be Published
Title: Structural Function of the Methionine-Rich Beta-Hairpin in the Laccase for T. Thermophilus.
Authors: Jimenez-Arroyo, N. / Cardona-Felix, C.S. / Rojas-Trejo, S.P. / Rudino-Pinera, E.
History
DepositionJan 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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)51,04123
Polymers48,7911
Non-polymers2,24922
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.706, 110.579, 96.547
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-2101-

HOH

21A-2103-

HOH

31A-2228-

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
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 HB27 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q4H436, UniProt: Q72HW2*PLUS, laccase

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Non-polymers , 6 types, 400 molecules

#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / 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.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ag
#5: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#6: Chemical ChemComp-OH / HYDROXIDE ION


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


Mass: 18.015 Da / Num. of mol.: 378 / 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 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: 2.56 Å3/Da / Density % sol: 52.93 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M HEPES PH 7.5, 70 % MPD BEFORE DATA COLLECTION THE CRYSTAL WAS SOAKED FOR 30 MINUTES IN 5 MM AGNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 16, 2013
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: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.19→29.35 Å / Num. obs: 25637 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 17.14 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.1
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.6 / % possible all: 88.5

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Processing

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

2xu9


Resolution: 2.193→29.346 Å / SU ML: 0.18 / σ(F): 1.4 / Phase error: 16.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 1302 5.1 %
Rwork0.146 --
obs0.1484 25617 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.76 Å2
Refinement stepCycle: LAST / Resolution: 2.193→29.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 120 378 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093915
X-RAY DIFFRACTIONf_angle_d1.3335374
X-RAY DIFFRACTIONf_dihedral_angle_d15.4371525
X-RAY DIFFRACTIONf_chiral_restr0.067585
X-RAY DIFFRACTIONf_plane_restr0.007702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1929-2.28070.21191160.15882335X-RAY DIFFRACTION86
2.2807-2.38450.22431590.15032692X-RAY DIFFRACTION100
2.3845-2.51010.19851530.15852706X-RAY DIFFRACTION100
2.5101-2.66730.22161510.15832713X-RAY DIFFRACTION100
2.6673-2.87310.21471440.15392731X-RAY DIFFRACTION100
2.8731-3.16190.19951630.14372716X-RAY DIFFRACTION100
3.1619-3.61870.17891360.13562759X-RAY DIFFRACTION100
3.6187-4.55640.14651310.12442782X-RAY DIFFRACTION100
4.5564-29.34850.20881490.15872881X-RAY DIFFRACTION100

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