5NFJ | pdb_00005nfj

Crystal structure of the methyltransferase subunit of human mitochondrial Ribonuclease P (MRPP1) bound to S-adenosyl-methionine (SAM)

PDB DOI: https://doi.org/10.2210/pdb5NFJ/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-03-14 Released: 2018-05-16
Deposition Author(s): Oerum, S., Kopec, J., Fitzpatrick, F., Newman, J.A., Chalk, R., Shrestha, L., Fairhead, M., Talon, R., Burgess-Brown, N., von Delft, F., Arrowsmith, C., Edwards, C., Bountra, C., Oppermann, U., Yue, W.W., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.206 (Depositor), 0.213 (DCC)
R-Value Work:
0.185 (Depositor)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the methyltransferase subunit of human mitochondrial Ribonuclease P (MRPP1) bound to S-adenosyl-methionine (SAM)

Oerum, S., Kopec, J., Fitzpatrick, F., Newman, J.A., Oppermann, U., Yue, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 73.49 kDa
Atom Count: 4,772
Modeled Residue Count: 533
Deposited Residue Count: 606
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial ribonuclease P protein 1	A, B, C	202	Homo sapiens	Mutation(s): 0 Gene Names: TRMT10C, MRPP1, RG9MTD1 EC: 2.1.1 (PDB Primary Data), 2.1.1.221 (UniProt), 2.1.1.218 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L0Y3 (Homo sapiens) Explore Q7L0Y3 Go to UniProtKB: Q7L0Y3
PHAROS: Q7L0Y3 GTEx: ENSG00000174173
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7L0Y3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain P [auth C] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain P [auth C] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B], P [auth C]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] K [auth B] L [auth B] E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], M [auth B], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], N [auth B], O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.206 (Depositor), 0.213 (DCC)
R-Value Work: 0.185 (Depositor)
R-Value Observed: 0.186 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.64	α = 90
b = 82.64	β = 90
c = 148.62	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHELXD	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-05-08
Changes: Advisory, Data collection, Database references