[English] 日本語
Yorodumi
- PDB-6vw4: 2.35 Angstrom structure of Caci_6494 from Catenulispora Acidiphil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vw4
Title2.35 Angstrom structure of Caci_6494 from Catenulispora Acidiphila in complex with S-DNPA
ComponentsAromatic-ring-hydroxylating dioxygenase beta subunit
KeywordsUNKNOWN FUNCTION / NTF2 Superfamily
Function / homologySnoaL-like domain / SnoaL-like domain / dioxygenase activity / NTF2-like domain superfamily / Chem-SDN / Aromatic-ring-hydroxylating dioxygenase beta subunit
Function and homology information
Biological speciesCatenulispora acidiphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsVuksanovic, N. / Silvaggi, N.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Structural characterization of three noncanonical NTF2-like superfamily proteins: implications for polyketide biosynthesis.
Authors: Vuksanovic, N. / Zhu, X. / Serrano, D.A. / Siitonen, V. / Metsa-Ketela, M. / Melancon 3rd, C.E. / Silvaggi, N.R.
History
DepositionFeb 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Sep 2, 2020Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aromatic-ring-hydroxylating dioxygenase beta subunit
B: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3493
Polymers35,0632
Non-polymers2861
Water1,47782
1
A: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules

A: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules

A: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4536
Polymers52,5943
Non-polymers8593
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area5540 Å2
ΔGint-46 kcal/mol
Surface area17690 Å2
MethodPISA
2
B: Aromatic-ring-hydroxylating dioxygenase beta subunit

B: Aromatic-ring-hydroxylating dioxygenase beta subunit

B: Aromatic-ring-hydroxylating dioxygenase beta subunit


Theoretical massNumber of molelcules
Total (without water)52,5943
Polymers52,5943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area5580 Å2
ΔGint-45 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.240, 161.240, 161.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21B-209-

HOH

31B-235-

HOH

-
Components

#1: Protein Aromatic-ring-hydroxylating dioxygenase beta subunit


Mass: 17531.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catenulispora acidiphila (strain DSM 44928 / NRRL B-24433 / NBRC 102108 / JCM 14897) (bacteria)
Strain: DSM 44928 / NRRL B-24433 / NBRC 102108 / JCM 14897 / Gene: Caci_6494 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C7PWR4
#2: Chemical ChemComp-SDN / [(3S)-9-hydroxy-1-methyl-10-oxo-4,10-dihydro-3H-benzo[g]isochromen-3-yl]acetic acid / 4,10-dihydro-9-hydroxy-1-methyl-10-oxo-3-H-naphtho-[2,3-c]-pyran-3-(S)-acetic acid


Mass: 286.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.47 M K2HPO4, 0.07 M NaH2PO4, 5% PEG 400, pH 8.3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→65.83 Å / Num. obs: 29103 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 43.9 Å2 / Rrim(I) all: 0.1 / Net I/σ(I): 11.4
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 2846 / Rrim(I) all: 0.68

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P77

6p77


Resolution: 2.35→57.007 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.91
RfactorNum. reflection% reflection
Rfree0.2279 1445 4.97 %
Rwork0.198 --
obs0.1994 29061 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.04 Å2 / Biso mean: 56.7606 Å2 / Biso min: 21.36 Å2
Refinement stepCycle: final / Resolution: 2.35→57.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 34 82 2190
Biso mean--82.65 50.01 -
Num. residues----269
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.351-2.4350.35721200.26262761100
2.435-2.53240.27191730.24792702100
2.5324-2.64770.29471630.22862727100
2.6477-2.78730.23161490.2042734100
2.7873-2.96190.21441580.19972740100
2.9619-3.19060.24841420.20982750100
3.1906-3.51160.28031160.20522783100
3.5116-4.01970.2391660.18632742100
4.0197-5.06390.17321210.15872825100
5.0639-57.0070.19611370.2114285299

+
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://pdbjlvh1.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