[English] 日本語
Yorodumi
- PDB-6ssg: Transaminase with DCS bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ssg
TitleTransaminase with DCS bound
ComponentsForI-DCS
KeywordsTRANSFERASE / DCS bound
Function / homologyChem-LUK
Function and homology information
Biological speciesStreptomyces kaniharaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsNaismith, J.H. / Gao, S.
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: PMP-diketopiperazine adducts form at the active site of a PLP dependent enzyme involved in formycin biosynthesis.
Authors: Gao, S. / Liu, H. / de Crecy-Lagard, V. / Zhu, W. / Richards, N.G.J. / Naismith, J.H.
History
DepositionSep 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 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: ForI-DCS
B: ForI-DCS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,55310
Polymers89,1102
Non-polymers1,4438
Water14,988832
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-122 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.060, 127.080, 141.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 425
2010B2 - 425

-
Components

#1: Protein ForI-DCS


Mass: 44555.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces kaniharaensis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-LUK / [4-[(~{Z})-[(2~{R},5~{R})-5-(azanyloxymethyl)-3,6-bis(oxidanylidene)piperazin-2-yl]methoxyiminomethyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate


Mass: 433.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N5O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200 mM Li2SO4, 100 mM Tris-HCl pH 8.0 and 30 % (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.47→61.73 Å / Num. obs: 174068 / % possible obs: 97.9 % / Redundancy: 33.1 % / CC1/2: 1 / Net I/σ(I): 13.9
Reflection shellResolution: 1.47→1.5 Å / Num. unique obs: 8486 / CC1/2: 0.7

-
Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→61.73 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.62 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.054
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1699 8763 5 %RANDOM
Rwork0.1447 ---
obs0.146 165228 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 159.35 Å2 / Biso mean: 21.507 Å2 / Biso min: 7.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2--1.1 Å20 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 1.47→61.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6254 0 88 832 7174
Biso mean--42.91 34.24 -
Num. residues----848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136748
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176185
X-RAY DIFFRACTIONr_angle_refined_deg1.321.6439220
X-RAY DIFFRACTIONr_angle_other_deg1.4041.57814313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555905
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.1221.3323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.074151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9631550
X-RAY DIFFRACTIONr_chiral_restr0.0750.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027907
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021431
X-RAY DIFFRACTIONr_rigid_bond_restr0.806312933
Refine LS restraints NCS

Ens-ID: 1 / Number: 13858 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.47→1.508 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 627 -
Rwork0.306 11902 -
all-12529 -
obs--96.16 %

+
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