[English] 日本語
Yorodumi
- PDB-4hn0: Crystal Structure of ChmJ, a 3'-monoepimerase apoenzyme from Stre... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hn0
TitleCrystal Structure of ChmJ, a 3'-monoepimerase apoenzyme from Streptomyces bikiniensis
ComponentsPutative 3-epimerase in D-allose pathway
KeywordsUNKNOWN FUNCTION / 3'-monoepimerase / natural product / deoxysugar / chalcomycin / dTDP-mycinose / Cupin fold / nucleotide-linked sugar / Epimerization
Function / homology
Function and homology information


dTDP-4-dehydro-6-deoxy-D-glucose 3-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / antibiotic biosynthetic process / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
dTDP-4-dehydro-6-deoxyglucose 3-epimerase
Similarity search - Component
Biological speciesStreptomyces bikiniensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHolden, H.M. / Kubiak, R.L.
CitationJournal: Biochemistry / Year: 2012
Title: Structural and Functional Studies on a 3'-Epimerase Involved in the Biosynthesis of dTDP-6-deoxy-d-allose.
Authors: Kubiak, R.L. / Phillips, R.K. / Zmudka, M.W. / Ahn, M.R. / Maka, E.M. / Pyeatt, G.L. / Roggensack, S.J. / Holden, H.M.
History
DepositionOct 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative 3-epimerase in D-allose pathway
B: Putative 3-epimerase in D-allose pathway
C: Putative 3-epimerase in D-allose pathway
D: Putative 3-epimerase in D-allose pathway
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,68420
Polymers87,7984
Non-polymers88716
Water3,855214
1
A: Putative 3-epimerase in D-allose pathway
B: Putative 3-epimerase in D-allose pathway
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,52813
Polymers43,8992
Non-polymers63011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-4 kcal/mol
Surface area16750 Å2
MethodPISA
2
C: Putative 3-epimerase in D-allose pathway
D: Putative 3-epimerase in D-allose pathway
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1567
Polymers43,8992
Non-polymers2575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-16 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.587, 141.587, 115.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein
Putative 3-epimerase in D-allose pathway


Mass: 21949.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces bikiniensis (bacteria) / Gene: chmJ / Plasmid: pET-31b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q5SFD1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 3.3 Å3/Da / Density % sol: 62.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3400, 2% 2-methyl-2,4-pentanediol, 100 mM MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 4, 2012
RadiationMonochromator: double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→100.12 Å / Num. obs: 53594 / % possible obs: 96 % / Redundancy: 6.7 %
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.74 / Num. unique all: 9437 / Rsym value: 0.43 / % possible all: 89.3

-
Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HMZ

4hmz


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.953 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25871 2917 5.2 %RANDOM
Rwork0.2149 ---
obs0.21724 53594 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6187 0 52 214 6453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216399
X-RAY DIFFRACTIONr_angle_refined_deg2.241.9438715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2365789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00923.103319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76415935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3881560
X-RAY DIFFRACTIONr_chiral_restr0.1590.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215064
X-RAY DIFFRACTIONr_mcbond_it1.5591.53946
X-RAY DIFFRACTIONr_mcangle_it2.75426346
X-RAY DIFFRACTIONr_scbond_it4.40832453
X-RAY DIFFRACTIONr_scangle_it6.8044.52368
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 205 -
Rwork0.265 3776 -
obs--94.14 %

+
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