[English] 日本語
Yorodumi
- PDB-4k7t: Structure of the ternary complex of bacitracin, zinc, and geranyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k7t
TitleStructure of the ternary complex of bacitracin, zinc, and geranyl-pyrophosphate
Componentsbacitracin A2
KeywordsANTIBIOTIC / bacitracin / cell-wall biosynthesis inhibitor / undecaprenyl-pyrophosphate
Function / homologyBacitracin A1 / GERANYL DIPHOSPHATE / :
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsEconomou, N.J. / Loll, P.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: High-resolution crystal structure reveals molecular details of target recognition by bacitracin.
Authors: Economou, N.J. / Cocklin, S. / Loll, P.J.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Oct 16, 2013Group: Derived calculations

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: bacitracin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8634
Polymers1,4611
Non-polymers4033
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.980, 35.980, 16.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

-
Components

#1: Protein/peptide bacitracin A2


Type: Cyclic peptide / Class: Antibiotic / Mass: 1460.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: NOR: NOR00018, Bacitracin A1
#2: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O7P2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Compound detailsILE-1 AND CYS-2 HAVE UNDERGONE A CONDENSATION REACTION TO PRODUCE A THIAZOLINE RING

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 6.5
Details: 20% PEG-2000 in 0.1 M sodium acetate pH 6.5, microbatch under oil, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Details: Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionNumber: 115240 / Rmerge(I) obs: 0.086 / D res high: 1.29 Å / Num. obs: 5949 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1.291.3244095.910.642
1.321.3643099.810.511
1.361.3939510010.367
1.391.4442510010.315
1.441.4838910010.223
1.481.5436110010.183
1.541.5939110010.147
1.591.6633210010.122
1.661.7335310010.093
1.731.8231710010.089
1.821.9230310010.086
1.922.0330010010.069
2.032.1727710010.07
2.172.3525810010.066
2.352.5723610010.067
2.572.8720599.510.062
2.873.3219210010.059
3.324.0716110010.055
4.075.7512110010.062
ReflectionResolution: 1.1→12.005 Å / Num. obs: 4983 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 11.547 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.69
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.1-1.160.6694.1144461423199.9
1.16-1.240.4156.451531114621100
1.24-1.340.24110.21453213711100
1.34-1.470.15914.471367212751100
1.47-1.640.10919.711190311041100
1.64-1.890.07725.02106549901100
1.89-2.310.06232.0790628531100
2.31-3.240.05635.076783647199.8
3.24-200.06138.783738363199.5

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→12.005 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8966 / SU ML: 0.08 / σ(F): 1.22 / Phase error: 17.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1493 438 4.62 %random
Rwork0.1271 ---
obs0.1284 4983 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 30.95 Å2 / Biso mean: 12.6637 Å2 / Biso min: 5.78 Å2
Refinement stepCycle: LAST / Resolution: 1.1→12.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms100 0 21 20 141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008121
X-RAY DIFFRACTIONf_angle_d2.051164
X-RAY DIFFRACTIONf_chiral_restr0.1216
X-RAY DIFFRACTIONf_plane_restr0.00519
X-RAY DIFFRACTIONf_dihedral_angle_d15.38139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.1-1.2590.16331160.137630443160
1.259-1.58560.13391710.112829913162
1.5856-12.00610.15451510.130430073158

+
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