3VET

Crystal structure of the O-carbamoyltransferase TobZ in complex with Tobramycin, carbamoyl phosphate and ADP

PDB DOI: https://doi.org/10.2210/pdb3VET/pdb

Classification: TRANSFERASE/ANTIBIOTIC
Organism(s): Streptoalloteichus tenebrarius
Expression System: Streptomyces lividans TK24
Mutation(s): Yes

Deposited: 2012-01-09 Released: 2012-01-25
Deposition Author(s): Parthier, C., Stubbs, M.T., Goerlich, S., Jaenecke, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.204 (Depositor), 0.200 (DCC)
R-Value Work:
0.165 (Depositor), 0.160 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction.

Parthier, C., Gorlich, S., Jaenecke, F., Breithaupt, C., Brauer, U., Fandrich, U., Clausnitzer, D., Wehmeier, U.F., Bottcher, C., Scheel, D., Stubbs, M.T.

(2012) Angew Chem Int Ed Engl 51: 4046-4052

PubMed: 22383337 Search on PubMed
DOI: https://doi.org/10.1002/anie.201108896
Primary Citation of Related Structures:
3VEN, 3VEO, 3VER, 3VES, 3VET, 3VEW, 3VEX, 3VEZ, 3VF2, 3VF4, 4E1B

Organizational Affiliation

Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany.

Macromolecule Content

Total Structure Weight: 65.09 kDa
Atom Count: 4,798
Modelled Residue Count: 567
Deposited Residue Count: 576
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-carbamoyltransferase TobZ	A	576	Streptoalloteichus tenebrarius	Mutation(s): 1 Gene Names: tacA, tobZ EC: 2.1.3 (PDB Primary Data), 6.1.2.2 (UniProt)
UniProt
Find proteins for Q70IY1 (Streptoalloteichus tenebrarius (strain ATCC 17920 / DSM 40477 / JCM 4838 / CBS 697.72 / NBRC 16177 / NCIMB 11028 / NRRL B-12390 / A12253. 1 / ISP 5477)) Explore Q70IY1 Go to UniProtKB: Q70IY1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q70IY1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TOY Query on TOY Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TOBRAMYCIN C₁₈ H₃₇ N₅ O₉ NLVFBUXFDBBNBW-PBSUHMDJSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A]	B [auth A], D [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A]
CP Query on CP 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]	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER C H₄ N O₅ P FFQKYPRQEYGKAF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.204 (Depositor), 0.200 (DCC)
R-Value Work: 0.165 (Depositor), 0.160 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.818	α = 90
b = 98.818	β = 90
c = 280.908	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-01-25
Type: Initial release
Version 1.1: 2012-03-14
Changes: Database references
Version 1.2: 2012-05-02
Changes: Database references
Version 1.3: 2017-11-15
Changes: Refinement description
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description