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- PDB-2yaf: X-ray induced reduction of laccase from Thermus thermophilus HB27... -

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Basic information

Entry
Database: PDB / ID: 2yaf
TitleX-ray induced reduction of laccase from Thermus thermophilus HB27 (12. 5-25.0 percent dose)
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
COPPER (II) ION / HYDROXIDE ION / Laccase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 22, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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)50,77220
Polymers48,7911
Non-polymers1,98019
Water9,296516
1
A: LACCASE
hetero molecules

A: LACCASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,54340
Polymers97,5832
Non-polymers3,96138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8660 Å2
ΔGint-267 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.659, 110.324, 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-2064-

HOH

21A-2070-

HOH

31A-2202-

HOH

41A-2283-

HOH

51A-2383-

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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q72HW2, laccase

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Non-polymers , 5 types, 535 molecules

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


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: 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
#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: Chemical ChemComp-OH / HYDROXIDE ION


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


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE AT THE UNIPROT DEPOSIT Q72HW2 POSITION 53 IS OCCUPIED BY A LEUCINE BUT THE ELECTRON ...THE SEQUENCE AT THE UNIPROT DEPOSIT Q72HW2 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: 8

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.82 % / 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: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→29 Å / Num. obs: 45193 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 11.28 Å2 / Rmerge(I) obs: 0.28 / Net I/σ(I): 6.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.5 / % possible all: 98.7

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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: 1.8→28.678 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 16.41 / Stereochemistry target values: ML
Details: HIS 95 WAS REFINED AS THE SINGLE MEMBER OF A TLS GROUP.
RfactorNum. reflection% reflection
Rfree0.189 2298 5.1 %
Rwork0.1544 --
obs0.1561 45193 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.069 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.0408 Å20 Å20 Å2
2--0.3094 Å20 Å2
3----0.2687 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 124 516 4079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114027
X-RAY DIFFRACTIONf_angle_d1.4275548
X-RAY DIFFRACTIONf_dihedral_angle_d17.9681549
X-RAY DIFFRACTIONf_chiral_restr0.09604
X-RAY DIFFRACTIONf_plane_restr0.006730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83920.231350.18872671X-RAY DIFFRACTION98
1.8392-1.88190.23021510.17712687X-RAY DIFFRACTION98
1.8819-1.9290.2121440.17292685X-RAY DIFFRACTION99
1.929-1.98110.21121210.16732710X-RAY DIFFRACTION99
1.9811-2.03940.18761520.16252702X-RAY DIFFRACTION99
2.0394-2.10520.22141370.14842671X-RAY DIFFRACTION98
2.1052-2.18040.19031510.14982686X-RAY DIFFRACTION98
2.1804-2.26770.1971370.14612708X-RAY DIFFRACTION98
2.2677-2.37090.2071460.1512659X-RAY DIFFRACTION98
2.3709-2.49580.18971450.15212717X-RAY DIFFRACTION98
2.4958-2.65210.1961550.15632653X-RAY DIFFRACTION98
2.6521-2.85670.17761480.15192719X-RAY DIFFRACTION98
2.8567-3.14380.19241480.1412681X-RAY DIFFRACTION97
3.1438-3.5980.15431590.13282649X-RAY DIFFRACTION96
3.598-4.53020.12161300.12442663X-RAY DIFFRACTION94
4.5302-28.68180.18491390.16482634X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: -16.0408 Å / Origin y: -19.8438 Å / Origin z: 3.7975 Å
111213212223313233
T-0.006 Å2-0.0387 Å2-0.0479 Å2--0.2721 Å2-0.2526 Å2---0.1193 Å2
L1.448 °2-1.186 °20.7863 °2-3.8757 °2-1.7002 °2--0.8107 °2
S0.0012 Å °-0.0101 Å °0.017 Å °0.0506 Å °0.0101 Å °-0.0074 Å °-0.0433 Å °0.0104 Å °0.007 Å °
Refinement TLS groupSelection details: CHAIN A AND RESID 95

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