[English] 日本語
Yorodumi
- PDB-6oyf: The structure of condensation and adenylation domains of teixobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oyf
TitleThe structure of condensation and adenylation domains of teixobactin-producing nonribosomal peptide synthetase Txo1 serine module
ComponentsTxo1
KeywordsBIOSYNTHETIC PROTEIN / Teixobactin / Nonribosomal Peptide Synthetase / Condensation domain / Adenylation Domain / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


toxin biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / catalytic activity / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. ...Methyltransferase type 12 / Methyltransferase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Biological speciesEleftheria terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsTan, K. / Zhou, M. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Curr Res Struct Biol / Year: 2020
Title: Structures of teixobactin-producing nonribosomal peptide synthetase condensation and adenylation domains.
Authors: Tan, K. / Zhou, M. / Jedrzejczak, R.P. / Wu, R. / Higuera, R.A. / Borek, D. / Babnigg, G. / Joachimiak, A.
History
DepositionMay 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Txo1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,47819
Polymers96,5661
Non-polymers1,91318
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-149 kcal/mol
Surface area37800 Å2
Unit cell
Length a, b, c (Å)152.965, 90.749, 98.218
Angle α, β, γ (deg.)90.00, 105.99, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Txo1


Mass: 96565.836 Da / Num. of mol.: 1
Fragment: Condensation and Adenylation Domain (UNP residues 2140-3009)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eleftheria terrae (bacteria) / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-Gold(DE3) / References: UniProt: A0A0B5GUD2, Transferases

-
Non-polymers , 6 types, 419 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES/sodium chloride, 1.26 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2016 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→43.5 Å / Num. obs: 75359 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.74 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.038 / Rrim(I) all: 0.071 / Χ2: 0.964 / Net I/σ(I): 20.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3719 / CC1/2: 0.629 / Rpim(I) all: 0.495 / Rrim(I) all: 0.916 / Χ2: 0.734 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.153 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.91
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 3285 4.96 %random
Rwork0.1863 ---
obs0.1876 66186 87.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6488 0 107 401 6996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026775
X-RAY DIFFRACTIONf_angle_d0.4859253
X-RAY DIFFRACTIONf_dihedral_angle_d21.1054029
X-RAY DIFFRACTIONf_chiral_restr0.0381013
X-RAY DIFFRACTIONf_plane_restr0.0041216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13140.2665600.2321279X-RAY DIFFRACTION41
2.1314-2.16470.2505700.21881577X-RAY DIFFRACTION50
2.1647-2.20010.2363790.21561738X-RAY DIFFRACTION56
2.2001-2.23810.24241020.21492012X-RAY DIFFRACTION65
2.2381-2.27880.241190.20772239X-RAY DIFFRACTION72
2.2788-2.32260.24761030.20462324X-RAY DIFFRACTION75
2.3226-2.370.2771380.21042547X-RAY DIFFRACTION83
2.37-2.42150.25511350.21772897X-RAY DIFFRACTION93
2.4215-2.47790.23271760.21093038X-RAY DIFFRACTION98
2.4779-2.53980.24211670.20473087X-RAY DIFFRACTION99
2.5398-2.60850.23811500.20033073X-RAY DIFFRACTION99
2.6085-2.68520.24371710.20463083X-RAY DIFFRACTION99
2.6852-2.77190.24071710.20863039X-RAY DIFFRACTION99
2.7719-2.87090.20661600.20693090X-RAY DIFFRACTION99
2.8709-2.98590.24721610.20313074X-RAY DIFFRACTION99
2.9859-3.12170.23451860.19543035X-RAY DIFFRACTION98
3.1217-3.28620.2351830.19923064X-RAY DIFFRACTION100
3.2862-3.49210.21111720.17913127X-RAY DIFFRACTION100
3.4921-3.76150.20211480.17073090X-RAY DIFFRACTION99
3.7615-4.13980.17321620.15363099X-RAY DIFFRACTION99
4.1398-4.73820.1591510.14763076X-RAY DIFFRACTION98
4.7382-5.96710.19761540.17023164X-RAY DIFFRACTION100
5.9671-43.1620.18931670.18373149X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6765-0.38910.2760.96170.84860.81890.21210.1539-0.3024-0.0805-0.4021-0.32691.68520.19170.20231.17070.36980.14921.22470.15080.675172.0743-36.014942.7391
25.0788-0.47630.82915.29061.57854.3236-0.1037-0.1264-0.64420.3305-0.3811-0.14621.98670.65040.42661.09390.31840.1811.05360.29470.751277.8132-40.603549.1991
31.00530.18960.29560.8345-0.4312.5884-0.1536-0.8172-0.15950.2008-0.302-0.44980.03991.00260.3230.29190.1135-0.09181.3050.36030.508584.6289-17.325242.1018
40.79840.10180.14710.21440.54391.5311-0.1646-0.6752-0.75-0.0507-0.2231-0.44360.81040.7753-0.040.42320.25040.02150.83270.44250.693482.3375-23.576328.6946
51.4415-0.50770.35551.253-0.5641.04790.03630.1093-0.02-0.1044-0.04740.0653-0.07040.08280.01270.15860.00370.01560.0911-0.03530.137947.951511.1155-2.9855
62.37210.0924-0.18553.0077-0.47590.71320.0810.1356-0.006-0.1257-0.0901-0.1255-0.05320.1058-0.00330.15490.024-0.00470.0943-0.04860.101549.19147.4152-3.1622
72.04540.27420.10521.0697-0.35571.06310.0012-0.21690.00440.0918-0.06470.01930.00040.07430.05410.14970.00690.00360.087-0.04770.136351.4639-1.02110.1793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2139 through 2189 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2190 through 2272 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2273 through 2485 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2486 through 2564 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2565 through 2729 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2730 through 2797 )
7X-RAY DIFFRACTION7chain 'A' and (resid 2798 through 3002 )

+
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