[English] 日本語
Yorodumi
- PDB-5kah: Crystal structure of a dioxygenase in the Crotonase superfamily i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kah
TitleCrystal structure of a dioxygenase in the Crotonase superfamily in P21, V425T mutant
Components(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / dioxygenase / DpgC
Function / homology
Function and homology information


(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid beta-oxidation / antibiotic biosynthetic process / identical protein binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1300 / : / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Complex / Up-down Bundle ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1300 / : / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-YE1 / (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
Similarity search - Component
Biological speciesStreptomyces toyocaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.779 Å
AuthorsLi, K. / Fielding, E.N. / Condurso, H.L. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086570 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase.
Authors: Li, K. / Fielding, E.N. / Condurso, H.L. / Bruner, S.D.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
B: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
C: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
D: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
E: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
F: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
G: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
H: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
I: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
J: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
K: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
L: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)589,72524
Polymers578,91712
Non-polymers10,80712
Water13,295738
1
A: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
B: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
C: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
J: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
K: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
L: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,86212
Polymers289,4596
Non-polymers5,4046
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27040 Å2
ΔGint-83 kcal/mol
Surface area91880 Å2
MethodPISA
2
D: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
E: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
F: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
G: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
H: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
I: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,86212
Polymers289,4596
Non-polymers5,4046
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27420 Å2
ΔGint-95 kcal/mol
Surface area91600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.772, 171.958, 156.111
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
(3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase


Mass: 48243.105 Da / Num. of mol.: 12 / Mutation: V425T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces toyocaensis (bacteria) / Gene: BU52_01220 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8KLK7, (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase
#2: Chemical
ChemComp-YE1 / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE


Mass: 900.615 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C29H43N8O19P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 140 mM ammonium acetate, 14% w/v PEG 4,000, and 100 mM sodium citrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.779→39.028 Å / Num. obs: 184721 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.14 / Net I/σ(I): 11.8
Reflection shellResolution: 2.779→2.83 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.6 / % possible all: 89.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NP9

2np9


Resolution: 2.779→39.028 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.75 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.231 9419 5.1 %
Rwork0.1976 --
obs0.2029 184687 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.779→39.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39122 0 708 738 40568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00440586
X-RAY DIFFRACTIONf_angle_d0.86455062
X-RAY DIFFRACTIONf_dihedral_angle_d17.88315298
X-RAY DIFFRACTIONf_chiral_restr0.0496092
X-RAY DIFFRACTIONf_plane_restr0.0057220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7797-2.82760.35564630.27638474X-RAY DIFFRACTION92
2.8276-2.8790.31264780.26618745X-RAY DIFFRACTION95
2.879-2.93440.34084290.25438700X-RAY DIFFRACTION95
2.9344-2.99430.29934800.2478827X-RAY DIFFRACTION95
2.9943-3.05930.31234240.2448753X-RAY DIFFRACTION95
3.0593-3.13050.29694420.24118811X-RAY DIFFRACTION95
3.1305-3.20870.27924430.2368719X-RAY DIFFRACTION95
3.2087-3.29540.25574480.22588770X-RAY DIFFRACTION95
3.2954-3.39230.27054630.21558825X-RAY DIFFRACTION95
3.3923-3.50170.24984760.21858752X-RAY DIFFRACTION95
3.5017-3.62680.24164850.21748726X-RAY DIFFRACTION95
3.6268-3.77190.25044340.2038811X-RAY DIFFRACTION95
3.7719-3.94340.22454630.19118747X-RAY DIFFRACTION95
3.9434-4.1510.225180.18998734X-RAY DIFFRACTION94
4.151-4.41070.20234550.17538781X-RAY DIFFRACTION95
4.4107-4.75070.18575040.16228780X-RAY DIFFRACTION95
4.7507-5.22760.1785300.16338754X-RAY DIFFRACTION94
5.2276-5.98150.23294680.18498814X-RAY DIFFRACTION95
5.9815-7.52610.19824990.18338813X-RAY DIFFRACTION95
7.5261-37.59020.17635020.16918930X-RAY DIFFRACTION95

+
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