3D4E | pdb_00003d4e

Crystal structure of putative beta-lactamase inhibitor protein (NP_721579.1) from STREPTOCOCCUS MUTANS at 1.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3D4E/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus mutans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-14 Released: 2008-07-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of putative beta-lactamase inhibitor protein (NP_721579.1) from STREPTOCOCCUS MUTANS at 1.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.4 kDa 
• Atom Count: 1,529 
• Modeled Residue Count: 162 
• Deposited Residue Count: 179 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative beta-lactamase inhibitor protein	A	179	Streptococcus mutans	Mutation(s): 0  Gene Names: NP_721579.1, SMU_1196c
UniProt
Find proteins for Q8DTX1 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DTX1  Go to UniProtKB:  Q8DTX1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33D4E

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.695	α = 90
b = 28.373	β = 90.01
c = 32.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-07-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-09
  Changes: Data collection, Structure summary