[English] 日本語
Yorodumi
- PDB-5g3e: Preserving Metallic Sites Affected by Radiation DAmage the CuT2 C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g3e
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 / 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: 1.78 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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THERMUS THERMOPHILUS MULTICOPPER OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,18715
Polymers48,7911
Non-polymers1,39514
Water8,827490
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 area5970 Å2
ΔGint-171.6 kcal/mol
Surface area32850 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-2290-

HOH

21A-2295-

HOH

31A-2375-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein THERMUS THERMOPHILUS MULTICOPPER OXIDASE


Mass: 48791.457 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-462 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / References: UniProt: I7AL37, UniProt: Q72HW2*PLUS, laccase

-
Non-polymers , 5 types, 504 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.: 490 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

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

-
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: 1.75→19.72 Å / Num. obs: 313136 / % possible obs: 98.3 % / Observed criterion σ(I): 18.25 / Redundancy: 6.3 % / Biso Wilson estimate: 11.97 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.05 / % possible all: 96.9

-
Processing

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

2yae


Resolution: 1.78→19.7 Å / SU ML: 0.15 / σ(F): 1.36 / Phase error: 15.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1775 2339 4.9 %
Rwork0.1374 --
obs0.1393 47287 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 84 490 4013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164035
X-RAY DIFFRACTIONf_angle_d1.5295560
X-RAY DIFFRACTIONf_dihedral_angle_d15.9371582
X-RAY DIFFRACTIONf_chiral_restr0.119598
X-RAY DIFFRACTIONf_plane_restr0.01744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.81630.2141220.1632643X-RAY DIFFRACTION98
1.8163-1.85580.20131620.15172587X-RAY DIFFRACTION98
1.8558-1.89890.18641270.15412637X-RAY DIFFRACTION99
1.8989-1.94640.17971460.14732611X-RAY DIFFRACTION99
1.9464-1.99890.20481360.14692614X-RAY DIFFRACTION99
1.9989-2.05770.22341380.16292617X-RAY DIFFRACTION99
2.0577-2.1240.17641510.14022645X-RAY DIFFRACTION99
2.124-2.19990.171340.13622628X-RAY DIFFRACTION99
2.1999-2.28780.18731360.13462658X-RAY DIFFRACTION99
2.2878-2.39180.17741460.13462638X-RAY DIFFRACTION99
2.3918-2.51760.18581340.14342654X-RAY DIFFRACTION99
2.5176-2.6750.19891390.14232691X-RAY DIFFRACTION99
2.675-2.8810.17131290.13842648X-RAY DIFFRACTION99
2.881-3.16980.17541280.13282681X-RAY DIFFRACTION99
3.1698-3.6260.16741220.12612681X-RAY DIFFRACTION98
3.626-4.5590.11721310.11322664X-RAY DIFFRACTION97
4.559-19.70090.19191580.1432651X-RAY DIFFRACTION94

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more