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- PDB-5g3c: Preserving Metallic sites affected by radiation damage the CuT2 c... -

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Basic information

Entry
Database: PDB / ID: 5g3c
TitlePreserving Metallic sites affected by radiation damage the CuT2 case in thermus termophilus 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 / 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
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.0Jun 7, 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_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_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
Water9,764542
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 operation3_454-x-1,y,-z-1/21
Buried area6990 Å2
ΔGint-141.4 kcal/mol
Surface area33580 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-2157-

HOH

21A-2335-

HOH

31A-2340-

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, laccase

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Non-polymers , 5 types, 557 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.: 7 / 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.: 542 / 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: 2.57 Å3/Da / Density % sol: 52.12 % / 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: 1.62→19.72 Å / Num. obs: 393350 / % possible obs: 98.1 % / Observed criterion σ(I): 17 / Redundancy: 6.3 % / Biso Wilson estimate: 11.22 Å2 / Rmerge(I) obs: 0.09
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 6.3 % / % possible all: 96.1

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Processing

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

2yae


Resolution: 1.75→19.66 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 15.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1657 2464 5 %
Rwork0.1356 --
obs0.1371 49653 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 92 542 4073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194049
X-RAY DIFFRACTIONf_angle_d1.6685576
X-RAY DIFFRACTIONf_dihedral_angle_d16.2111578
X-RAY DIFFRACTIONf_chiral_restr0.129605
X-RAY DIFFRACTIONf_plane_restr0.011740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78360.19871170.15812597X-RAY DIFFRACTION98
1.7836-1.820.19181540.14942587X-RAY DIFFRACTION99
1.82-1.85960.20581490.14882596X-RAY DIFFRACTION99
1.8596-1.90280.20161280.15112601X-RAY DIFFRACTION99
1.9028-1.95030.22491270.14952614X-RAY DIFFRACTION99
1.9503-2.0030.17961410.14962600X-RAY DIFFRACTION99
2.003-2.06190.20971470.16092590X-RAY DIFFRACTION99
2.0619-2.12840.18031280.13942636X-RAY DIFFRACTION99
2.1284-2.20440.18751350.14032605X-RAY DIFFRACTION99
2.2044-2.29250.15681350.13142636X-RAY DIFFRACTION99
2.2925-2.39670.1661520.13162630X-RAY DIFFRACTION100
2.3967-2.52280.16061460.13712623X-RAY DIFFRACTION99
2.5228-2.68050.18251320.13782654X-RAY DIFFRACTION99
2.6805-2.88680.16511370.13272627X-RAY DIFFRACTION99
2.8868-3.17620.14841450.12422641X-RAY DIFFRACTION99
3.1762-3.63330.13881400.1222654X-RAY DIFFRACTION98
3.6333-4.56810.1191290.11182636X-RAY DIFFRACTION97
4.5681-19.66090.161220.1462662X-RAY DIFFRACTION94

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