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- PDB-5g3h: Preserving Metallic Sites Affected by Radiation Damage the CuT2 C... -

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Basic information

Entry
Database: PDB / ID: 5g3h
TitlePreserving Metallic Sites Affected by Radiation Damage the CuT2 Case in Thermus Thermophilus Multicopper oxidase
ComponentsTHERMUS THERMOPHILUS MULTICOPPER OXIDASE
KeywordsOXIDOREDUCTASE / MULTICOPPER OXIDASE / RADIATION DAMAGE / METALIC SITES / MACROMOLECULES 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
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsRuiz-Arellano, 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 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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 / _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)50,18715
Polymers48,7911
Non-polymers1,39514
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.744, 110.332, 96.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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

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Non-polymers , 5 types, 451 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.: 6 / 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.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#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.: 437 / 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: 1.88→19.72 Å / Num. obs: 40211 / % possible obs: 98.3 % / Observed criterion σ(I): 17.93 / Redundancy: 6.3 % / Biso Wilson estimate: 15.87 Å2 / Rmerge(I) obs: 0.09
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.48 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YAE

2yae


Resolution: 1.93→19.723 Å / SU ML: 0.16 / σ(F): 1.37 / Phase error: 17.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1898 1845 4.9 %
Rwork0.135 --
obs0.1377 37342 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→19.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 84 437 3960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184133
X-RAY DIFFRACTIONf_angle_d1.6475697
X-RAY DIFFRACTIONf_dihedral_angle_d18.8771614
X-RAY DIFFRACTIONf_chiral_restr0.106623
X-RAY DIFFRACTIONf_plane_restr0.01759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.98210.24811260.17172726X-RAY DIFFRACTION99
1.9821-2.04040.2351430.1772707X-RAY DIFFRACTION99
2.0404-2.10620.18911400.15052696X-RAY DIFFRACTION99
2.1062-2.18140.18431490.14132714X-RAY DIFFRACTION99
2.1814-2.26860.20421530.13952721X-RAY DIFFRACTION99
2.2686-2.37170.20181390.13692718X-RAY DIFFRACTION99
2.3717-2.49650.22371310.14012771X-RAY DIFFRACTION99
2.4965-2.65260.19441400.14462710X-RAY DIFFRACTION99
2.6526-2.85680.19991520.13842752X-RAY DIFFRACTION99
2.8568-3.14330.2121590.13222730X-RAY DIFFRACTION99
3.1433-3.59570.16021340.12052761X-RAY DIFFRACTION99
3.5957-4.52120.14681370.10812731X-RAY DIFFRACTION97
4.5212-19.72380.18511420.13632760X-RAY DIFFRACTION94

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