[English] 日本語
Yorodumi
- PDB-7rab: Crystal structure of a dodecameric multicopper oxidase from M. hy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rab
TitleCrystal structure of a dodecameric multicopper oxidase from M. hydrothermalis in a cubic lattice
Componentsmulticopper oxidase
KeywordsOXIDOREDUCTASE / multicopper oxidase thermophile dodecamer laccase
Function / homology
Function and homology information


nitrite reductase (NO-forming) / : / nitrite reductase (NO-forming) activity / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesMarinithermus hydrothermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsGeorgiadis, M.M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystal structures of a dodecameric multicopper oxidase from Marinithermus hydrothermalis.
Authors: Paavola, J.L. / Battistin, U. / Ogata, C.M. / Georgiadis, M.M.
History
DepositionJun 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: multicopper oxidase
B: multicopper oxidase
C: multicopper oxidase
D: multicopper oxidase
E: multicopper oxidase
F: multicopper oxidase
G: multicopper oxidase
H: multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,60932
Polymers315,3988
Non-polymers1,21124
Water11,151619
1
A: multicopper oxidase
C: multicopper oxidase
E: multicopper oxidase
H: multicopper oxidase
hetero molecules

A: multicopper oxidase
C: multicopper oxidase
E: multicopper oxidase
H: multicopper oxidase
hetero molecules

A: multicopper oxidase
C: multicopper oxidase
E: multicopper oxidase
H: multicopper oxidase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, The protein elutes with a molecular weight that is larger than a trimer but smaller than a hexamer. Within the asymmetric unit, there are 8 molecules; two trimers and two ...Evidence: gel filtration, The protein elutes with a molecular weight that is larger than a trimer but smaller than a hexamer. Within the asymmetric unit, there are 8 molecules; two trimers and two single subunits. These chains along with symmetry mates generate two dodecamers in the A.U. Each single subunit (chains F and A) with its symmetry mates comprises a second trimer. Symmetry mates of each trimer (CEH or BGD) make up the remaining two trimers that form a dodecamer.
  • 475 kDa, 12 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)474,91448
Polymers473,09712
Non-polymers1,81736
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
MethodPISA
2
B: multicopper oxidase
D: multicopper oxidase
F: multicopper oxidase
G: multicopper oxidase
hetero molecules

B: multicopper oxidase
D: multicopper oxidase
F: multicopper oxidase
G: multicopper oxidase
hetero molecules

B: multicopper oxidase
D: multicopper oxidase
F: multicopper oxidase
G: multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,91448
Polymers473,09712
Non-polymers1,81736
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPISA
Unit cell
Length a, b, c (Å)224.241, 224.241, 224.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11H-563-

HOH

-
Components

#1: Protein
multicopper oxidase /


Mass: 39424.773 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinithermus hydrothermalis (bacteria)
Gene: Marky_0543 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: F2NNS0, laccase
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M HEPES 7.5, 25% PEG 335
PH range: 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.37623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37623 Å / Relative weight: 1
ReflectionResolution: 1.915→129.47 Å / Num. obs: 284806 / % possible obs: 99.7 % / Redundancy: 39 % / Biso Wilson estimate: 27.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.028 / Rrim(I) all: 0.173 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.92-2.0240.21.6041665919414390.9620.2561.6252.5
6.06-129.4738.60.066362861941010.0110.06727.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GDC_A

Resolution: 1.92→56.06 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 43.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2983 13962 4.99 %
Rwork0.2701 265961 -
obs0.2715 279923 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.94 Å2 / Biso mean: 30.3317 Å2 / Biso min: 15.65 Å2
Refinement stepCycle: final / Resolution: 1.92→56.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19324 0 24 619 19967
Biso mean--47.81 32.46 -
Num. residues----2392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720176
X-RAY DIFFRACTIONf_angle_d0.89427544
X-RAY DIFFRACTIONf_dihedral_angle_d3.57215944
X-RAY DIFFRACTIONf_chiral_restr0.062776
X-RAY DIFFRACTIONf_plane_restr0.0073664
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.92-1.93690.39624420.3633898599
1.9369-1.95970.37444760.3461895499
1.9597-1.98360.3754200.3377900399
1.9836-2.00870.36844910.3366888299
2.0087-2.03510.37614880.3317895799
2.0351-2.0630.38054840.3317891099
2.063-2.09250.35554060.32639027100
2.0925-2.12370.34344730.3182889799
2.1237-2.15690.33464600.3119896999
2.1569-2.19230.32714540.3086884299
2.1923-2.23010.33294430.3029893099
2.2301-2.27060.34784540.2967891899
2.2706-2.31430.30965800.2935881699
2.3143-2.36150.32894960.2842885899
2.3615-2.41290.32344830.2865889999
2.4129-2.4690.33334840.2915884098
2.469-2.53070.35274610.2881883098
2.5307-2.59920.30284580.2902888398
2.5992-2.67560.32074290.2779881097
2.6756-2.7620.32594330.2823882397
2.762-2.86070.32015130.2746881498
2.8607-2.97530.31254780.2825877798
2.9753-3.11070.30684450.2847882397
3.1107-3.27460.31694350.2823874697
3.2746-3.47980.29674210.2715883897
3.4798-3.74840.28974420.262876996
3.7484-4.12550.24974790.233877897
4.1255-4.72220.23244440.2104879796
4.7222-5.94840.25475250.2206884197
5.9484-56.060.23154650.2244874593

+
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