3PEB

The Structure of a Creatine_N Superfamily domain of a dipeptidase from Streptococcus thermophilus.

PDB DOI: https://doi.org/10.2210/pdb3PEB/pdb

Classification: HYDROLASE
Organism(s): Streptococcus thermophilus LMG 18311
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-10-25 Released: 2010-11-03
Deposition Author(s): Cuff, M.E., Mack, J.C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.190
R-Value Work: 0.170
R-Value Observed: 0.171

wwPDB Validation 3D Report Full Report

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

Literature

The Structure of a Creatine_N Superfamily domain of a dipeptidase from Streptococcus thermophilus.

Cuff, M.E., Mack, J.C., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 16.69 kDa
Atom Count: 1,327
Modelled Residue Count: 132
Deposited Residue Count: 137
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidase	A	137	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: pepQ, stu0629
UniProt
Find proteins for Q5M567 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M567 Go to UniProtKB: Q5M567
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5M567
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NHE Query on NHE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO 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 A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	M [auth A], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [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: 1.86 Å
R-Value Free: 0.190
R-Value Work: 0.170
R-Value Observed: 0.171
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.503	α = 90
b = 70.503	β = 90
c = 160.388	γ = 120

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