3IKB | pdb_00003ikb

The structure of a conserved protein from Streptococcus mutans UA159.

PDB DOI: https://doi.org/10.2210/pdb3IKB/pdb

Classification: structural genomics, unknown function
Organism(s): Streptococcus mutans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-08-05 Released: 2009-08-18
Deposition Author(s): Tan, K., Hatzos, C., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.214 (Depositor), 0.223 (DCC)
R-Value Work:
0.185 (Depositor), 0.196 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3IKB

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

Literature

The structure of a conserved protein from Streptococcus mutans UA159.

Tan, K., Hatzos, C., Buck, K., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 46.85 kDa
Atom Count: 3,825
Modeled Residue Count: 392
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized conserved protein	A, B	198	Streptococcus mutans	Mutation(s): 0 Gene Names: SMU_1238c, Streptococcus mutans
UniProt
Find proteins for Q8DTT5 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DTT5 Go to UniProtKB: Q8DTT5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DTT5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	C [auth A], D [auth A], E [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [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: 1.67 Å
R-Value Free: 0.214 (Depositor), 0.223 (DCC)
R-Value Work: 0.185 (Depositor), 0.196 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.372	α = 90
b = 66.372	β = 90
c = 197.818	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-08-18

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-20
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.