[English] 日本語
Yorodumi
- PDB-4jel: Structure of MilB Streptomyces rimofaciens CMP N-glycosidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jel
TitleStructure of MilB Streptomyces rimofaciens CMP N-glycosidase
ComponentsCMP/hydroxymethyl CMP hydrolase
KeywordsHYDROLASE / CMP N-glycosidase / mildiomycin biosynthesis
Function / homologyNucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CMP/hydroxymethyl CMP hydrolase
Function and homology information
Biological speciesStreptomyces rimofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.952 Å
AuthorsSikowitz, M.D. / Cooper, L.E. / Begley, T.P. / Kaminski, P.A. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2013
Title: Reversal of the substrate specificity of CMP N-glycosidase to dCMP.
Authors: Sikowitz, M.D. / Cooper, L.E. / Begley, T.P. / Kaminski, P.A. / Ealick, S.E.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CMP/hydroxymethyl CMP hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7413
Polymers20,5491
Non-polymers1922
Water1,946108
1
A: CMP/hydroxymethyl CMP hydrolase
hetero molecules

A: CMP/hydroxymethyl CMP hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4836
Polymers41,0982
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+11
Buried area3020 Å2
ΔGint-80 kcal/mol
Surface area13140 Å2
MethodPISA
2
A: CMP/hydroxymethyl CMP hydrolase
hetero molecules

A: CMP/hydroxymethyl CMP hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4836
Polymers41,0982
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+5/31
Buried area1980 Å2
ΔGint-61 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.819, 97.819, 61.893
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-340-

HOH

31A-406-

HOH

-
Components

#1: Protein CMP/hydroxymethyl CMP hydrolase


Mass: 20549.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rimofaciens (bacteria) / Gene: MilB / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: B4Y381
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 8% PEG 1000, 0.1 M phosphate-citrate, 0.2 M lithium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2010
RadiationMonochromator: Cryo-cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 24181 / Num. obs: 23697 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 27.96 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 40.1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.95-1.98196.9
1.98-2.02197.8
2.02-2.06196.7
2.06-2.1197.9
2.1-2.15197.7
2.15-2.2197.5

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.952→42.357 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8582 / SU ML: 0.18 / σ(F): 1.89 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 1168 4.93 %random
Rwork0.1981 ---
obs0.2002 23688 98.27 %-
all-23697 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.42 Å2 / Biso mean: 26.5855 Å2 / Biso min: 12.43 Å2
Refinement stepCycle: LAST / Resolution: 1.952→42.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1149 0 10 108 1267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071183
X-RAY DIFFRACTIONf_angle_d1.0831607
X-RAY DIFFRACTIONf_chiral_restr0.071176
X-RAY DIFFRACTIONf_plane_restr0.005212
X-RAY DIFFRACTIONf_dihedral_angle_d11.833417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9524-2.04120.24211670.19872780294797
2.0412-2.14880.22831630.18912753291698
2.1488-2.28350.24311550.19262802295798
2.2835-2.45970.24711220.19352836295898
2.4597-2.70720.2491460.20032804295098
2.7072-3.09890.23861560.20412824298099
3.0989-3.90380.23731310.19592843297499
3.9038-42.36680.25251280.20052878300699

+
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