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- PDB-5g3b: Preserving metallic sites affected by radiation damage: the CuT2 ... -

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Basic information

Entry
Database: PDB / ID: 5g3b
TitlePreserving metallic sites affected by radiation damage: the CuT2 case in Thermus thermophilus multicopper oxidase
ComponentsTHERMUS THERMOPHILUS MULTICOPPER OXIDASE
KeywordsOXIDOREDUCTASE / MULTICOPPER OXIDASE / RADIATION DAMAGE / METALLIC SITES / MACROMOLECULAR CRYSTALLOGRAPHY / RADICAL SCAVENGERS
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / outer membrane-bounded periplasmic space / 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
COPPER (II) ION / Copper oxidase / Laccase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsRuiz-Arellano, R.R. / Diaz, A. / Rosas, E. / Rudino, E.
CitationJournal: To be Published
Title: Preserving Metallic Sites Affected by Radiation Damage the Cut2 Case in Thermus Thermophilus Multicopper Oxidase
Authors: Ruiz-Arellano, R. / Diaz, A. / Rosas, E. / Stojanoff, V. / Rudino, E.
History
DepositionApr 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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: THERMUS THERMOPHILUS MULTICOPPER OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,30516
Polymers48,7911
Non-polymers1,51415
Water10,142563
1
A: THERMUS THERMOPHILUS MULTICOPPER OXIDASE
hetero molecules

A: THERMUS THERMOPHILUS MULTICOPPER OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,61032
Polymers97,5832
Non-polymers3,02730
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area7990 Å2
ΔGint-242 kcal/mol
Surface area32320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.744, 110.332, 96.484
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-2079-

HOH

21A-2360-

HOH

31A-2365-

HOH

41A-2445-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein THERMUS THERMOPHILUS MULTICOPPER OXIDASE


Mass: 48791.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: I7AL37, UniProt: Q72HW2*PLUS, laccase

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Non-polymers , 5 types, 578 molecules

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


Mass: 118.174 Da / Num. of mol.: 5 / 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.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.89 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→19.72 Å / Num. obs: 64734 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 10.58 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.6→1.66 Å / % possible all: 96

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Processing

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

2yae


Resolution: 1.69→19.687 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 16.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1789 2728 5 %
Rwork0.139 --
obs0.1409 54990 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→19.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 92 563 4094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184068
X-RAY DIFFRACTIONf_angle_d1.5845601
X-RAY DIFFRACTIONf_dihedral_angle_d15.8941590
X-RAY DIFFRACTIONf_chiral_restr0.112604
X-RAY DIFFRACTIONf_plane_restr0.01747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.72070.2131500.16032759X-RAY DIFFRACTION98
1.7207-1.75380.2241170.15382688X-RAY DIFFRACTION98
1.7538-1.78960.1881320.15142739X-RAY DIFFRACTION98
1.7896-1.82850.19171300.1532730X-RAY DIFFRACTION98
1.8285-1.8710.20331450.15222715X-RAY DIFFRACTION98
1.871-1.91770.19141470.14792714X-RAY DIFFRACTION99
1.9177-1.96950.19081440.14422760X-RAY DIFFRACTION99
1.9695-2.02740.19831530.16132709X-RAY DIFFRACTION99
2.0274-2.09280.21261410.14842752X-RAY DIFFRACTION99
2.0928-2.16750.17491550.14032756X-RAY DIFFRACTION99
2.1675-2.25420.171360.13572758X-RAY DIFFRACTION99
2.2542-2.35660.17921300.13832788X-RAY DIFFRACTION99
2.3566-2.48060.19391590.13962767X-RAY DIFFRACTION99
2.4806-2.63570.21021520.14832757X-RAY DIFFRACTION99
2.6357-2.83860.18241610.14132763X-RAY DIFFRACTION99
2.8386-3.12330.16721450.13252775X-RAY DIFFRACTION99
3.1233-3.57290.16751570.12662775X-RAY DIFFRACTION98
3.5729-4.49260.12921470.11392762X-RAY DIFFRACTION97
4.4926-19.68790.17081270.13972795X-RAY DIFFRACTION94

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