[English] 日本語
Yorodumi
- PDB-9khp: The crystal structure of XhnM1 with SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9khp
TitleThe crystal structure of XhnM1 with SAH
ComponentsClass I SAM-dependent methyltransferase
KeywordsTRANSFERASE / methyl group / Xinhaicarxin BG
Function / homology
Function and homology information


biosynthetic process / methyltransferase activity / methylation
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ACETATE ION / CYSTEINE / S-ADENOSYL-L-HOMOCYSTEINE / Class I SAM-dependent methyltransferase
Similarity search - Component
Biological speciesStreptomyces xinghaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73006100024 Å
AuthorsWu, L. / Tang, G.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Targeted Discovery and Characterization of Type-II PKS-NRPS Hybrid DNA-Alkylating Antibiotics.
Authors: Nie, Q.Y. / Fang, S.Q. / Wu, L. / Gao, R.Q. / Hu, Y. / Ding, D. / Pan, H.X. / Pei, Z.F. / He, J.B. / Zhou, Q. / Chen, Z.H. / Hou, X.F. / Zhao, X.Q. / Tang, G.L.
History
DepositionNov 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Class I SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5407
Polymers29,7731
Non-polymers7676
Water3,657203
1
A: Class I SAM-dependent methyltransferase
hetero molecules

A: Class I SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,08114
Polymers59,5472
Non-polymers1,53412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area3640 Å2
ΔGint-19 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.990, 124.320, 69.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Class I SAM-dependent methyltransferase


Mass: 29773.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces xinghaiensis (bacteria) / Gene: Sfr7A_13950, SFRA_005385 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3R7FZU3

-
Non-polymers , 6 types, 209 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M imidazole hydrochloride acid pH 8.0,0.2 M calcium acetate, and 10% pEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.73→46.450163 Å / Num. obs: 27619 / % possible obs: 98.4 % / Redundancy: 13.3 % / Biso Wilson estimate: 23.8497643409 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Net I/σ(I): 17.8
Reflection shellResolution: 1.74→1.83 Å / Rmerge(I) obs: 0.94 / Num. unique obs: 3887 / CC1/2: 0.878

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73006100024→46.4501629927 Å / SU ML: 0.145262600305 / Cross valid method: FREE R-VALUE / σ(F): 1.34362631118 / Phase error: 19.2753525329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.203326918856 1347 4.87760718424 %
Rwork0.177775340518 26269 -
obs0.179048283691 27616 98.1518339494 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.5872662042 Å2
Refinement stepCycle: LAST / Resolution: 1.73006100024→46.4501629927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 49 203 2185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006327398103522023
X-RAY DIFFRACTIONf_angle_d0.9173667198872750
X-RAY DIFFRACTIONf_chiral_restr0.0544578733308294
X-RAY DIFFRACTIONf_plane_restr0.00587783715403374
X-RAY DIFFRACTIONf_dihedral_angle_d20.20975120491189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7301-1.79190.2685308841151220.2353228958992568X-RAY DIFFRACTION96.9369369369
1.7919-1.86360.2472928265481350.2156673316712548X-RAY DIFFRACTION97.528171574
1.8636-1.94850.2342678816421370.1983287291642573X-RAY DIFFRACTION97.4119338605
1.9485-2.05120.2163343294391450.1816715090912591X-RAY DIFFRACTION97.7491961415
2.0512-2.17970.2082443859991300.168006618962607X-RAY DIFFRACTION97.8198713367
2.1797-2.3480.2056825806981370.1700936866462611X-RAY DIFFRACTION98.2130092924
2.348-2.58430.2371665466131320.1834911816152622X-RAY DIFFRACTION98.3220278472
2.5843-2.95820.207232251761240.1839993700132647X-RAY DIFFRACTION98.9996427295
2.9582-3.72670.180071344111330.1663518179222701X-RAY DIFFRACTION99.194959748
3.7267-46.450162990.179417808071520.1674873522422801X-RAY DIFFRACTION99.2605042017

+
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