6AC6 | pdb_00006ac6

Ab initio crystal structure of Selenomethionine labelled Mycobacterium smegmatis Mfd

PDB DOI: https://doi.org/10.2210/pdb6AC6/pdb

Classification: HYDROLASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-07-25 Released: 2019-08-28
Deposition Author(s): Putta, S., Fox, G.C., Walsh, M.A., Rao, D.N., Nagaraja, V., Natesh, R.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free:
0.270 (Depositor), 0.274 (DCC)
R-Value Work:
0.218 (Depositor), 0.223 (DCC)
R-Value Observed:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6AC6

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

Literature

Structural basis for nucleotide-mediated remodelling mechanism of Mycobacterium Mfd

Putta, S., Prabha, S., Bhat, V., Fox, G.C., Walsh, M.A., Rao, D.N., Nagaraja, V., Natesh, R.

To be published.

Macromolecule Content

Total Structure Weight: 269.89 kDa
Atom Count: 16,853
Modeled Residue Count: 2,307
Deposited Residue Count: 2,470
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycobacterium smegmatis Mfd	A, B	1,235	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: mfd EC: 3.6.4
UniProt
Find proteins for A0R3C5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R3C5 Go to UniProtKB: A0R3C5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0R3C5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free: 0.270 (Depositor), 0.274 (DCC)
R-Value Work: 0.218 (Depositor), 0.223 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.71	α = 90
b = 158.87	β = 90
c = 207.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
CRANK2	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	India	BT/HRD/35/02/19/2009

Revision History (Full details and data files)

Version 1.0: 2019-08-28
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Structure summary

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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.