6CN0 | pdb_00006cn0

2.95 Angstrom Crystal Structure of 16S rRNA Methylase from Proteus mirabilis

PDB DOI: https://doi.org/10.2210/pdb6CN0/pdb

Classification: TRANSFERASE
Organism(s): Proteus mirabilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-03-06 Released: 2018-03-21
Deposition Author(s): Minasov, G., Wawrzak, Z., Di Leo, R., Evdokimova, E., Savchenko, A., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.263 (Depositor), 0.262 (DCC)
R-Value Work:
0.218 (Depositor), 0.216 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6CN0

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

Literature

2.95 Angstrom Crystal Structure of 16S rRNA Methylase from Proteus mirabilis.

Minasov, G., Wawrzak, Z., Di Leo, R., Evdokimova, E., Savchenko, A., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 130.48 kDa
Atom Count: 8,611
Modeled Residue Count: 1,058
Deposited Residue Count: 1,136
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
16S rRNA (guanine(1405)-N(7))-methyltransferase	A, B, C, D	284	Proteus mirabilis	Mutation(s): 0 Gene Names: rmtC EC: 2.1.1.179
UniProt
Find proteins for Q33DX5 (Proteus mirabilis) Explore Q33DX5 Go to UniProtKB: Q33DX5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q33DX5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	E [auth A] H [auth B] I [auth C] J [auth C] K [auth D] E [auth A], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.263 (Depositor), 0.262 (DCC)
R-Value Work: 0.218 (Depositor), 0.216 (DCC)
R-Value Observed: 0.220 (Depositor)

Diffraction Data:

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.318	α = 90
b = 158.318	β = 90
c = 122.892	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Satchell, K.J.F.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-03-21
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, 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.