[English] 日本語
Yorodumi
- PDB-9nst: Bacterial Pictet-Spenglerase KslB in complex with product of L-Tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nst
TitleBacterial Pictet-Spenglerase KslB in complex with product of L-Trp and a-ketoglutaric acid
ComponentsPictet-Spenglerase
KeywordsBIOSYNTHETIC PROTEIN / Pictet-Spenglerase
Function / homologyCucumopine synthase, C-terminal helical bundle domain / Cucumopine synthase C-terminal helical bundle domain / : / Cucumopine synthase C-terminal helical bundle domain-containing protein
Function and homology information
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKim, K. / Kim, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA281106 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM148356 United States
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Structural and mechanistic insights into KslB, a bacterial Pictet-Spenglerase in kitasetaline biosynthesis.
Authors: Kim, W. / Zheng, Z. / Kim, K. / Lee, Y.H. / Liu, H.W. / Zhang, Y.J.
History
DepositionMar 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pictet-Spenglerase
B: Pictet-Spenglerase
C: Pictet-Spenglerase
D: Pictet-Spenglerase
E: Pictet-Spenglerase
F: Pictet-Spenglerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,40010
Polymers211,0706
Non-polymers1,3294
Water00
1
A: Pictet-Spenglerase
B: Pictet-Spenglerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0214
Polymers70,3572
Non-polymers6652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-51 kcal/mol
Surface area21650 Å2
MethodPISA
2
C: Pictet-Spenglerase
D: Pictet-Spenglerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0214
Polymers70,3572
Non-polymers6652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-47 kcal/mol
Surface area20810 Å2
MethodPISA
3
E: Pictet-Spenglerase
F: Pictet-Spenglerase


Theoretical massNumber of molelcules
Total (without water)70,3572
Polymers70,3572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-50 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.569, 95.569, 193.651
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

-
Components

#1: Protein
Pictet-Spenglerase / Cucumopine synthase C-terminal helical bundle domain-containing protein


Mass: 35178.398 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora setae (bacteria) / Gene: KSE_70640 / Production host: Escherichia coli (E. coli) / References: UniProt: E4NIM4
#2: Chemical
ChemComp-A1L46 / (1~{S},3~{S})-1-(3-hydroxy-3-oxopropyl)-2,3,4,9-tetrahydropyrido[3,4-b]indole-1,3-dicarboxylic acid


Mass: 332.308 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H16N2O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 3350, Sodium chloride, Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.48
ReflectionResolution: 3.3→47.78 Å / Num. obs: 29279 / % possible obs: 98.9 % / Redundancy: 2.9 % / CC1/2: 0.942 / Net I/σ(I): 6.1
Reflection shellResolution: 3.3→3.39 Å / Num. unique obs: 1400 / CC1/2: 0.346

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→47.78 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.7971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2133 2065 7.16 %
Rwork0.1943 26772 -
obs0.2009 28837 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.14 Å2
Refinement stepCycle: LAST / Resolution: 3.3→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14123 0 96 0 14219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002414591
X-RAY DIFFRACTIONf_angle_d0.52819989
X-RAY DIFFRACTIONf_chiral_restr0.03942263
X-RAY DIFFRACTIONf_plane_restr0.01032578
X-RAY DIFFRACTIONf_dihedral_angle_d15.775233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.390.25991380.25071795X-RAY DIFFRACTION85.93
3.39-3.480.27111380.23681846X-RAY DIFFRACTION88.37
3.48-3.580.25081480.22341915X-RAY DIFFRACTION89.32
3.58-3.70.25821390.20681921X-RAY DIFFRACTION90.31
3.7-3.830.2611480.2071933X-RAY DIFFRACTION90.24
3.83-3.980.25291420.20381913X-RAY DIFFRACTION90.62
3.98-4.160.20351450.19411919X-RAY DIFFRACTION90.9
4.16-4.380.23031520.19441904X-RAY DIFFRACTION90.8
4.38-4.660.21851340.17931943X-RAY DIFFRACTION92.79
4.66-5.010.18581570.18841986X-RAY DIFFRACTION91.73
5.02-5.520.18191440.18451915X-RAY DIFFRACTION91.54
5.52-6.320.23571390.21151961X-RAY DIFFRACTION91.94
6.32-7.940.20911490.19061922X-RAY DIFFRACTION90.49
7.96-47.780.16061470.19051944X-RAY DIFFRACTION92.4

+
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