[English] 日本語
Yorodumi
- PDB-5tii: Comprehensive Analysis of a Novel Ketoreductase for Pentangular P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tii
TitleComprehensive Analysis of a Novel Ketoreductase for Pentangular Polyphenol Biosynthesis
Components3-oxoacyl-ACP reductase
KeywordsOXIDOREDUCTASE / Arixanthomycin / Pentangular polyphenol Polyketide / Ketoreduction
Function / homology
Function and homology information


monocarboxylic acid metabolic process / lipid metabolic process / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 3-oxoacyl-ACP reductase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsValentic, T.R. / Tsai, S.C. / Brady, S.F.
CitationJournal: ACS Chem. Biol. / Year: 2016
Title: Comprehensive Analysis of a Novel Ketoreductase for Pentangular Polyphenol Biosynthesis.
Authors: Valentic, T.R. / Jackson, D.R. / Brady, S.F. / Tsai, S.C.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Oct 4, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-ACP reductase
D: 3-oxoacyl-ACP reductase
E: 3-oxoacyl-ACP reductase
G: 3-oxoacyl-ACP reductase
H: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
C: 3-oxoacyl-ACP reductase
F: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,71611
Polymers232,4808
Non-polymers2,2363
Water7,945441
1
A: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
C: 3-oxoacyl-ACP reductase
F: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,7316
Polymers116,2404
Non-polymers1,4912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15950 Å2
ΔGint-74 kcal/mol
Surface area33760 Å2
MethodPISA
2
D: 3-oxoacyl-ACP reductase
E: 3-oxoacyl-ACP reductase
G: 3-oxoacyl-ACP reductase
H: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9855
Polymers116,2404
Non-polymers7451
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15010 Å2
ΔGint-72 kcal/mol
Surface area32010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.380, 86.650, 107.320
Angle α, β, γ (deg.)90.00, 108.97, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
3-oxoacyl-ACP reductase


Mass: 29059.971 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: arx21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A023PKG5
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium Acetate and 30-32% PEG 4000 / Temp details: Room temp. At UCI Natural Sciences I Rm 2302

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→99.66 Å / Num. obs: 54103 / % possible obs: 96.1 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.6
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.932 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VL8

1vl8


Resolution: 2.6→52.671 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1959 3.72 %
Rwork0.1771 --
obs0.1793 52666 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→52.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14302 0 144 441 14887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414680
X-RAY DIFFRACTIONf_angle_d0.81919905
X-RAY DIFFRACTIONf_dihedral_angle_d18.9545245
X-RAY DIFFRACTIONf_chiral_restr0.0482336
X-RAY DIFFRACTIONf_plane_restr0.0032536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.66510.29371360.19733360X-RAY DIFFRACTION88
2.6651-2.73710.30181320.20023384X-RAY DIFFRACTION88
2.7371-2.81770.26231270.20243339X-RAY DIFFRACTION86
2.8177-2.90860.29481350.19983548X-RAY DIFFRACTION92
2.9086-3.01260.27431390.19743635X-RAY DIFFRACTION94
3.0126-3.13320.29771430.19583655X-RAY DIFFRACTION95
3.1332-3.27570.24381430.19243714X-RAY DIFFRACTION96
3.2757-3.44840.26861370.18563726X-RAY DIFFRACTION96
3.4484-3.66440.22651410.17113477X-RAY DIFFRACTION90
3.6644-3.94730.19241450.15713757X-RAY DIFFRACTION97
3.9473-4.34430.21011460.15583839X-RAY DIFFRACTION99
4.3443-4.97260.16521480.14153808X-RAY DIFFRACTION98
4.9726-6.26330.24041410.18583657X-RAY DIFFRACTION93
6.2633-52.68170.22111460.18493808X-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