3CED | pdb_00003ced

Crystal structure of the C-terminal NIL domain of an ABC transporter protein homologue from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3CED/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-02-28 Released: 2008-05-13
Deposition Author(s): Cuff, M.E., Bigelow, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.215 (Depositor), 0.210 (DCC)
R-Value Work:
0.184 (Depositor), 0.181 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3CED

This is version 1.3 of the entry. See complete history.

Literature

The structure of the C-terminal NIL domain of an ABC transporter protein homologue from Staphylococcus aureus.

Cuff, M.E., Bigelow, L., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 33.42 kDa
Atom Count: 2,731
Modeled Residue Count: 294
Deposited Residue Count: 294
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine import ATP-binding protein metN 2	A, B, C	98	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0 Gene Names: metN2, SAV0837 EC: 3.6.3 (PDB Primary Data), 7.4.2.11 (UniProt)
UniProt
Find proteins for Q99VG8 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q99VG8 Go to UniProtKB: Q99VG8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99VG8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BU1 Query on BU1 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth C] SDF format, chain G [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C]	D [auth A], E [auth A], F [auth C], G [auth C]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth C] Focus chain G [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth C] Focus chain G [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.215 (Depositor), 0.210 (DCC)
R-Value Work: 0.184 (Depositor), 0.181 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.55	α = 90
b = 132.55	β = 90
c = 132.083	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-05-13

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-05-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, 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.