[English] 日本語
Yorodumi
- PDB-9k0b: Structure of Pictet-Spenglerases KslB in complex with L-Trp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9k0b
TitleStructure of Pictet-Spenglerases KslB in complex with L-Trp
ComponentsCucumopine synthase C-terminal helical bundle domain-containing protein
KeywordsLIGASE / Pictet-Spenglerases / Kitasetalic acid
Function / homologyCucumopine synthase, C-terminal helical bundle domain / Cucumopine synthase C-terminal helical bundle domain / TRYPTOPHAN / Cucumopine synthase C-terminal helical bundle domain-containing protein
Function and homology information
Biological speciesKitasatospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMori, T. / Renata, H. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Pictet-Spenglerases KslB
Authors: Mori, T. / Renata, H. / Abe, I.
History
DepositionOct 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cucumopine synthase C-terminal helical bundle domain-containing protein
B: Cucumopine synthase C-terminal helical bundle domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1084
Polymers74,7002
Non-polymers4082
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-48 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.768, 82.102, 91.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

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


Mass: 37349.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora (bacteria) / Gene: KSE_70640 / Production host: Escherichia coli (E. coli) / References: UniProt: E4NIM4
#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM calcium acetate, 100 mM cacodylate pH 6.0, and 12% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.98 Å / Num. obs: 36772 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 17.88 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.256 / Net I/σ(I): 5.9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3002 / CC1/2: 0.797 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.98 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2496 1992 5.43 %
Rwork0.2066 34706 -
obs0.2089 36698 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4519 0 30 379 4928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00174673
X-RAY DIFFRACTIONf_angle_d0.51776406
X-RAY DIFFRACTIONf_chiral_restr0.0408730
X-RAY DIFFRACTIONf_plane_restr0.004819
X-RAY DIFFRACTIONf_dihedral_angle_d13.64241652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.3021440.23752444X-RAY DIFFRACTION100
2.15-2.210.27091390.22312453X-RAY DIFFRACTION99.96
2.21-2.280.25641420.21132459X-RAY DIFFRACTION100
2.28-2.350.25951380.22122440X-RAY DIFFRACTION99.96
2.35-2.430.28161400.2222420X-RAY DIFFRACTION100
2.43-2.530.30611420.21532448X-RAY DIFFRACTION100
2.53-2.650.26541460.21862481X-RAY DIFFRACTION99.96
2.65-2.790.30331410.22072458X-RAY DIFFRACTION100
2.79-2.960.29591430.21932457X-RAY DIFFRACTION99.92
2.96-3.190.26881380.21572467X-RAY DIFFRACTION99.96
3.19-3.510.23591450.20342501X-RAY DIFFRACTION100
3.51-4.020.2281410.18362499X-RAY DIFFRACTION99.96
4.02-5.060.18611440.17872533X-RAY DIFFRACTION99.93
5.06-48.980.20821490.20422646X-RAY DIFFRACTION99.57

+
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