4FN6 | pdb_00004fn6

Structural Characterization of Thiaminase type II TenA from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb4FN6/pdb

Classification: TRANSCRIPTION
Organism(s): Staphylococcus aureus subsp. aureus MRSA252
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-06-19 Released: 2012-12-19
Deposition Author(s): Begum, A., Drebes, J., Perbandt, M., Wrenger, C., Betzel, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free:
0.258 (Depositor), 0.255 (DCC)
R-Value Work:
0.213 (Depositor), 0.211 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural Characterization of Thiaminase type II TenA from Staphylococcus aureus

Begum, A., Drebes, J., Perbandt, M., Wrenger, C., Betzel, C.

To be published.

Macromolecule Content

Total Structure Weight: 108.69 kDa
Atom Count: 7,598
Modeled Residue Count: 899
Deposited Residue Count: 916
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thiaminase-2	A, B, C, D	229	Staphylococcus aureus subsp. aureus MRSA252	Mutation(s): 0 Gene Names: tenA, SAR2183 EC: 3.5.99.2
UniProt
Find proteins for Q6GEY1 (Staphylococcus aureus (strain MRSA252)) Explore Q6GEY1 Go to UniProtKB: Q6GEY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6GEY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain G [auth A]	G [auth A], J [auth B], K [auth C], L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth B] I [auth B] M [auth C] E [auth A], F [auth A], H [auth B], I [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.258 (Depositor), 0.255 (DCC)
R-Value Work: 0.213 (Depositor), 0.211 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.276	α = 90
b = 104.061	β = 90
c = 109.451	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-12-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-12-19
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary