[English] 日本語
Yorodumi
- PDB-8p4g: Crystal structure of a multicopper oxidase 3F3 variant from Pyrob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p4g
TitleCrystal structure of a multicopper oxidase 3F3 variant from Pyrobaculum aerophilum
ComponentsMulticopper oxidase
KeywordsOXIDOREDUCTASE / hyperthermophiles / metallo-oxidases / laccases / enzyme engineering / biocatalysis
Function / homology
Function and homology information


oxidoreductase activity / copper ion binding / membrane
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Multicopper oxidase
Similarity search - Component
Biological speciesPyrobaculum aerophilum str. IM2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBorges, P.T. / Brissos, V. / Frazao, C. / Martins, L.O.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: J.Biol.Inorg.Chem. / Year: 2024
Title: Flexible active-site loops fine-tune substrate specificity of hyperthermophilic metallo-oxidases.
Authors: Brissos, V. / Borges, P.T. / Sancho, F. / Lucas, M.F. / Frazao, C. / Conzuelo, F. / Martins, L.O.
History
DepositionMay 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multicopper oxidase
B: Multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,14011
Polymers97,5962
Non-polymers5449
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-89 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.395, 128.395, 124.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Multicopper oxidase


Mass: 48797.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum str. IM2 (archaea)
Gene: PAE1888 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZWA8
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 2.0 M Ammonium sulfate, 0.1 M Sodium HEPES pH 7.5, and 2 % (v/v) PEG 400.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.59→73.45 Å / Num. obs: 32726 / % possible obs: 99.1 % / Redundancy: 5.5 % / CC1/2: 0.986 / Net I/σ(I): 7.48
Reflection shellResolution: 2.59→2.69 Å / Num. unique obs: 5178 / CC1/2: 0.322

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→73.45 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 500 1.53 %
Rwork0.2131 --
obs0.2138 32700 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→73.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6785 0 1 142 6928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026985
X-RAY DIFFRACTIONf_angle_d0.5779513
X-RAY DIFFRACTIONf_dihedral_angle_d16.6632571
X-RAY DIFFRACTIONf_chiral_restr0.0451048
X-RAY DIFFRACTIONf_plane_restr0.0041239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.850.35291240.3367914X-RAY DIFFRACTION99
2.85-3.270.35231280.28087981X-RAY DIFFRACTION100
3.27-4.110.20231260.20368070X-RAY DIFFRACTION100
4.11-73.450.25141220.16818235X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0904-0.52881.22892.16430.18792.07940.11840.159-0.2822-0.13910.01690.02650.31540.0488-0.10380.5219-0.01490.0140.47250.02140.4343-42.7267-1.1917-22.2536
20.8913-0.14960.92082.0755-1.75193.673-0.0099-0.0451-0.00620.03480.01350.009-0.1218-0.1644-0.02850.4014-0.0152-0.00740.5645-0.02280.422-46.622911.4081-11.3783
31.74180.111-0.26731.87750.52061.6885-0.003-0.15160.1570.08440.1037-0.0671-0.05630.2617-0.07810.37360.0133-0.02190.5342-0.01490.3862-39.031511.7761-0.7481
41.39420.2911-1.12861.9445-0.68872.580.0649-0.0314-0.0702-0.0015-0.1121-0.40830.02670.50290.07940.3801-0.0283-0.08570.5697-0.04910.5669-26.51918.2114-12.2828
51.87650.09050.42082.048-0.01993.04170.01050.04630.1119-0.14190.025-0.4838-0.08310.4834-0.04660.3683-0.0190.07120.49280.02220.5184-25.452512.5427-20.1031
61.8863-0.06950.59851.368-0.56042.47610.0143-0.2818-0.01790.00490.00160.277-0.0532-0.3177-0.00060.4637-0.008-0.04810.4794-0.02120.4751-69.958420.7118-35.0106
71.5878-0.3494-0.19050.8928-0.30632.46590.130.03010.0803-0.1211-0.079-0.0509-0.0459-0.0175-0.02080.4889-00.0090.351-0.00080.4133-59.82324.5544-52.1058
83.93962.27132.90674.9824.32876.4948-0.16270.36590.1577-0.20860.24-0.3508-0.14860.7785-0.02670.48570.01670.06260.49010.08020.4307-49.692224.757-55.7099
90.71320.20020.29882.09730.88622.8979-0.04870.03270.2086-0.25-0.04930.1263-0.6182-0.01120.05330.57260.01740.07770.5804-0.00310.6478-64.341238.6047-45.0074
102.3565-0.49070.060.7915-0.17933.28480.0882-0.27730.4732-0.1093-0.03180.0608-0.4787-0.1239-0.03960.5463-0.0462-0.01140.3996-0.05710.5491-60.326140.6146-37.2223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 38:154)
2X-RAY DIFFRACTION2(chain A and resid 155:208)
3X-RAY DIFFRACTION3(chain A and resid 209:318)
4X-RAY DIFFRACTION4(chain A and resid 319:357)
5X-RAY DIFFRACTION5(chain A and resid 358:477)
6X-RAY DIFFRACTION6(chain B and resid 38:154)
7X-RAY DIFFRACTION7(chain B and resid 155:278)
8X-RAY DIFFRACTION8(chain B and resid 279:318)
9X-RAY DIFFRACTION9(chain B and resid 319:357)
10X-RAY DIFFRACTION10(chain B and resid 358:477)

+
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