[English] 日本語
Yorodumi
- PDB-9kyn: artificial dinuclear Cu-bound metalloprotein 3 (D3:Cu) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kyn
Titleartificial dinuclear Cu-bound metalloprotein 3 (D3:Cu)
ComponentsdTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsISOMERASE / Thermophilic isomerase
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
COPPER (II) ION / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJeong, W.J. / Song, W.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other private2019R1C1C1003863 Korea, Republic Of
CitationJournal: To Be Published
Title: Metal-Installer: A protein designer tool to create metal-binding sites
Authors: Jeong, W.J. / Song, W.J.
History
DepositionDec 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dTDP-4-dehydrorhamnose 3,5-epimerase
B: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9734
Polymers42,8462
Non-polymers1272
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.900, 52.498, 60.802
Angle α, β, γ (deg.)110.83, 107.43, 95.81
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein dTDP-4-dehydrorhamnose 3,5-epimerase / Thymidine diphospho-4-keto-rhamnose 3 / 5-epimerase / dTDP-4-keto-6-deoxyglucose 3 / dTDP-6-deoxy-D- ...Thymidine diphospho-4-keto-rhamnose 3 / 5-epimerase / dTDP-4-keto-6-deoxyglucose 3 / dTDP-6-deoxy-D-xylo-4-hexulose 3 / dTDP-L-rhamnose synthase


Mass: 21422.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rmlC, MTH_1790 / Production host: Escherichia coli (E. coli)
References: UniProt: O27818, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Li2SO4, 20 % PEG 4000, pH 8.0 0.1M MOPS

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00311 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00311 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 20609 / % possible obs: 96.6 % / Redundancy: 3.2 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.071 / Rrim(I) all: 0.131 / Χ2: 3.015 / Net I/σ(I): 9.6 / Num. measured all: 65431
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.342.60.3410570.8930.9710.2330.4140.67495.3
2.34-2.382.70.35110060.8780.9670.2370.4250.67795.6
2.38-2.432.90.32810180.8920.9710.220.3960.68996.5
2.43-2.482.90.3310670.8960.9720.220.3980.69696.8
2.48-2.533.10.3110050.9060.9750.2030.3720.82696.7
2.53-2.593.10.29310280.9070.9750.1910.3510.93297.1
2.59-2.653.20.26610560.9240.980.1720.3181.13296.9
2.65-2.733.30.25410020.9320.9820.1620.3021.13697.1
2.73-2.813.30.23510440.9470.9860.150.281.19396.6
2.81-2.93.30.18910280.9620.990.1190.2241.58696.4
2.9-33.20.16410220.9710.9930.1070.1971.51196.4
3-3.1230.13810020.9680.9920.0950.1691.90795.1
3.12-3.263.20.12510490.9760.9940.080.1492.40196.9
3.26-3.433.60.10910480.980.9950.0680.1292.67698.3
3.43-3.653.50.11510370.9810.9950.070.1353.55798.1
3.65-3.933.50.08810350.9880.9970.0560.1054.04697.5
3.93-4.333.40.07910560.9840.9960.050.0944.56198.1
4.33-4.953.20.08110110.9810.9950.0520.0966.48994
4.95-6.2330.0769900.9710.9930.0520.09310.03994.6
6.23-103.40.0810480.9790.9950.0520.09611.32597.8

-
Processing

Software
NameVersionClassification
PHENIX1.21.1.5286refinement
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.93 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 940 4.57 %
Rwork0.1991 --
obs0.2011 20573 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 2 15 3041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083104
X-RAY DIFFRACTIONf_angle_d0.8664206
X-RAY DIFFRACTIONf_dihedral_angle_d19.9881152
X-RAY DIFFRACTIONf_chiral_restr0.057430
X-RAY DIFFRACTIONf_plane_restr0.008562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.30091320.23362737X-RAY DIFFRACTION94
2.42-2.570.29571510.23832789X-RAY DIFFRACTION97
2.57-2.770.29381300.2362856X-RAY DIFFRACTION97
2.77-3.050.27991480.22712780X-RAY DIFFRACTION96
3.05-3.490.23151210.20162828X-RAY DIFFRACTION97
3.49-4.40.24091280.18082856X-RAY DIFFRACTION98
4.4-100.19351300.17712787X-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