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- PDB-5g3f: Preserving Metallic Sites Affected by Radiation Damage the CuT2 C... -

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Basic information

Entry
Database: PDB / ID: 5g3f
TitlePreserving Metallic Sites Affected by Radiation Damage the CuT2 CAse in Thermus Thermophilus Multicopper Oxidase
ComponentsTHERMUS THERMOPHILUS MULTICOPPER OXIDASE
KeywordsOXIDOREDUCTASE / MULTICOPPER OXIDASA / RADIATION DAMAGE / METALLIC SITES / MACROMOLECULAR CRYSTALLOGRAPHY / RADICAL SCAVENGERS
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 / Copper oxidase / Laccase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 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_alt_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.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
Water6,575365
1
A: THERMUS THERMOPHILUS MULTICOPPER OXIDASE
hetero molecules

A: THERMUS THERMOPHILUS MULTICOPPER OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,37430
Polymers97,5832
Non-polymers2,79128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area7180 Å2
ΔGint-207.7 kcal/mol
Surface area32990 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-2223-

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, 379 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.: 365 / 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: 1.79→19.72 Å / Num. obs: 292656 / % possible obs: 98.4 % / Observed criterion σ(I): 19.25 / Redundancy: 6.3 % / Biso Wilson estimate: 12.87 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.79→1.86 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.04 / % possible all: 97.3

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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: 1.82→19.707 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 16.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1789 2179 4.9 %
Rwork0.1463 --
obs0.148 44333 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→19.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 84 365 3888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084137
X-RAY DIFFRACTIONf_angle_d1.0315703
X-RAY DIFFRACTIONf_dihedral_angle_d16.0261630
X-RAY DIFFRACTIONf_chiral_restr0.063614
X-RAY DIFFRACTIONf_plane_restr0.006763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.85950.20241310.16242626X-RAY DIFFRACTION99
1.8595-1.90280.21091480.16232600X-RAY DIFFRACTION99
1.9028-1.95030.2251360.15662612X-RAY DIFFRACTION99
1.9503-2.0030.20211190.16152628X-RAY DIFFRACTION99
2.003-2.06190.19861380.17382597X-RAY DIFFRACTION99
2.0619-2.12840.19711390.14612639X-RAY DIFFRACTION99
2.1284-2.20430.18851270.14992626X-RAY DIFFRACTION99
2.2043-2.29250.15681370.14792635X-RAY DIFFRACTION99
2.2925-2.39660.20971290.14722649X-RAY DIFFRACTION99
2.3966-2.52270.16661170.15612664X-RAY DIFFRACTION99
2.5227-2.68040.20731270.15422681X-RAY DIFFRACTION99
2.6804-2.88680.17381550.14732612X-RAY DIFFRACTION99
2.8868-3.17620.15611440.14592644X-RAY DIFFRACTION99
3.1762-3.63330.17151410.13872655X-RAY DIFFRACTION98
3.6333-4.56820.15611490.11962632X-RAY DIFFRACTION97
4.5682-19.7080.16891420.14442654X-RAY DIFFRACTION94

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