7D8D | pdb_00007d8d

The crystal structure of ScNTM1 in complex with SAH and Rps25a hexapeptide

PDB DOI: https://doi.org/10.2210/pdb7D8D/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-08 Released: 2021-05-26
Deposition Author(s): Zhang, H.Y., Yue, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free:
0.136 (Depositor), 0.135 (DCC)
R-Value Work:
0.118 (Depositor), 0.118 (DCC)
R-Value Observed:
0.119 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural Basis for Peptide Binding of Alpha-N Terminal Methyltransferase from Saccharomyces cerevisiae

Zhang, H.Y., Kuang, Z., Xue, L., Yue, J., Khan, M.H., Zhu, Z., Niu, L.

(2021) Crystallogr Rep 66: 1316-1321

DOI: https://doi.org/10.1134/S1063774521070257

Macromolecule Content

Total Structure Weight: 27.19 kDa
Atom Count: 2,305
Modeled Residue Count: 238
Deposited Residue Count: 238
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha N-terminal protein methyltransferase 1	A	232	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: TAE1, NTM1, YBR261C, YBR1729 EC: 2.1.1.244
UniProt
Find proteins for P38340 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38340 Go to UniProtKB: P38340
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38340
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rps25A-peptide	B [auth D]	6	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E792 Go to UniProtKB: Q3E792
Entity Groups
UniProt Group	Q3E792
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.136 (Depositor), 0.135 (DCC)
R-Value Work: 0.118 (Depositor), 0.118 (DCC)
R-Value Observed: 0.119 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.692	α = 90
b = 52.014	β = 90
c = 127.723	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	U1632124 to L.N.
Ministry of Science and Technology (MoST, China)	China	2017YFA0503600 to L.N.

Revision History (Full details and data files)

Version 1.0: 2021-05-26
Type: Initial release
Version 1.1: 2021-12-29
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description

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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.