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- PDB-4ai7: Crystal structure of Laccase from Thermus thermophilus HB27 compl... -

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Basic information

Entry
Database: PDB / ID: 4ai7
TitleCrystal structure of Laccase from Thermus thermophilus HB27 complexed with Hg, crystal of the apoenzyme soaked for 2 h in 5 mM HgCl2 at 278 K.
ComponentsLACCASE-LIKE PROTEIN
KeywordsOXIDOREDUCTASE / MULTICOPPER OXIDASE
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / ferroxidase activity / outer membrane-bounded periplasmic space / 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, 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
: / Laccase-like protein / Laccase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSerrano-Posada, H. / 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
DepositionFeb 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2012Provider: 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-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,68522
Polymers48,7911
Non-polymers2,89421
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.276, 110.100, 96.214
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-2204-

HOH

21A-2309-

HOH

31A-2312-

HOH

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Components

#1: Protein LACCASE-LIKE 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 (bacteria) / Strain: HB27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q4H436, UniProt: Q72HW2*PLUS, 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.: 16 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.47 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 70 % MPD BEFORE DATA COLLECTION THE CRYSTAL WAS SOAKED FOR 2 HOURS IN 5 MM HGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 2, 2011
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: 1.7→28 Å / Num. obs: 53278 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 14.14 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.4
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.1 / % possible all: 97.5

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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→28.572 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 15.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1704 2695 5.1 %
Rwork0.152 --
obs0.1529 53273 97.44 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.367 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.1398 Å20 Å20 Å2
2---0.1993 Å20 Å2
3---0.0595 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 133 504 4076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134046
X-RAY DIFFRACTIONf_angle_d2.3225575
X-RAY DIFFRACTIONf_dihedral_angle_d17.8221563
X-RAY DIFFRACTIONf_chiral_restr0.095611
X-RAY DIFFRACTIONf_plane_restr0.007730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73090.22371220.22742654X-RAY DIFFRACTION97
1.7309-1.76420.26241500.21882626X-RAY DIFFRACTION97
1.7642-1.80020.23011340.1952621X-RAY DIFFRACTION97
1.8002-1.83930.2021240.18392651X-RAY DIFFRACTION98
1.8393-1.88210.19581520.1852634X-RAY DIFFRACTION98
1.8821-1.92920.20831320.16462653X-RAY DIFFRACTION98
1.9292-1.98130.21461670.16592624X-RAY DIFFRACTION98
1.9813-2.03960.20651520.16532654X-RAY DIFFRACTION98
2.0396-2.10540.19911490.15322647X-RAY DIFFRACTION98
2.1054-2.18070.19981170.15122711X-RAY DIFFRACTION98
2.1807-2.26790.1721420.15332670X-RAY DIFFRACTION99
2.2679-2.37110.18241370.14762686X-RAY DIFFRACTION99
2.3711-2.4960.17821530.14982691X-RAY DIFFRACTION98
2.496-2.65230.15951560.14642663X-RAY DIFFRACTION98
2.6523-2.85690.14291370.14042701X-RAY DIFFRACTION98
2.8569-3.14410.15811450.13662702X-RAY DIFFRACTION98
3.1441-3.59830.12971480.12742670X-RAY DIFFRACTION97
3.5983-4.53060.131530.11992662X-RAY DIFFRACTION96
4.5306-28.5760.1671250.16792658X-RAY DIFFRACTION91

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