4U1Q | pdb_00004u1q

Crystal structure of S-adenosylmethionine-dependent methyltransferase SibL in complex with 3HK and SAH

PDB DOI: https://doi.org/10.2210/pdb4U1Q/pdb

Classification: TRANSFERASE
Organism(s): Streptosporangium sibiricum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-16 Released: 2015-08-05
Deposition Author(s): liu, J.S., Chen, S.C., Yang, C.S., Huang, C.H., Chen, Y.
Funding Organization(s): National Science Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.213 (Depositor), 0.214 (DCC)
R-Value Work:
0.171 (Depositor), 0.173 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4U1Q

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of S-adenosylmethionine-dependent methyltransferase SibL in complex with 3HK and SAH

liu, J.S., Chen, S.C., Yang, C.S., Huang, C.H., Chen, Y.

To be published.

Macromolecule Content

Total Structure Weight: 158.13 kDa
Atom Count: 11,719
Modeled Residue Count: 1,364
Deposited Residue Count: 1,420
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SibL	A, B, C, D	355	Streptosporangium sibiricum	Mutation(s): 0 Gene Names: sibL
UniProt
Find proteins for C0LTM6 (Streptosporangium sibiricum) Explore C0LTM6 Go to UniProtKB: C0LTM6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C0LTM6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
3DJ Query on 3DJ Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	(2S)-2-amino-4-(2-amino-3-hydroxyphenyl)-4-oxobutanoic acid C₁₀ H₁₂ N₂ O₄ VCKPUUFAIGNJHC-LURJTMIESA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.213 (Depositor), 0.214 (DCC)
R-Value Work: 0.171 (Depositor), 0.173 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.304	α = 90
b = 112.783	β = 90
c = 143.139	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Council	Taiwan	NSC100-2313-B-241-006

Revision History (Full details and data files)

Version 1.0: 2015-08-05
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.