3BGK | pdb_00003bgk

The crystal structure of hypothetic protein SMU.573 from Streptococcus mutans

PDB DOI: https://doi.org/10.2210/pdb3BGK/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Streptococcus mutans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-26 Released: 2008-12-16
Deposition Author(s): Liang, Y.H., Zhou, Y.F., Yang, C., Su, X.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.256 (Depositor), 0.246 (DCC)
R-Value Work:
0.208 (Depositor), 0.201 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3BGK

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

Literature

The crystal structure of Streptococcus mutans protein SMU.573 solved from the anomalous signal measured with in-house chromium radiation

Liang, Y.H., Zhou, Y.F., Li, L.F., Su, X.D., Yang, C.

To be published.

Macromolecule Content

Total Structure Weight: 34.23 kDa
Atom Count: 2,043
Modeled Residue Count: 276
Deposited Residue Count: 311
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	311	Streptococcus mutans	Mutation(s): 0 Gene Names: SMU.573 EC: 4.2.1.136
UniProt
Find proteins for Q8DVC0 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DVC0 Go to UniProtKB: Q8DVC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DVC0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.256 (Depositor), 0.246 (DCC)
R-Value Work: 0.208 (Depositor), 0.201 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.527	α = 90
b = 96.527	β = 90
c = 56.26	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-12-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 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.