4EEC | pdb_00004eec

Crystal Structure of the glycopeptide antibiotic sulfotransferase StaL complexed with A3P and desulfo-A47934.

PDB DOI: https://doi.org/10.2210/pdb4EEC/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Streptomyces toyocaensis
Expression System: Escherichia coli BL21(DE3), Streptomyces toyocaensis
Mutation(s): No

Deposited: 2012-03-28 Released: 2012-07-04
Deposition Author(s): Shi, R., Cygler, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.272 (Depositor), 0.267 (DCC)
R-Value Work:
0.223 (Depositor), 0.215 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structural basis of sulfonation of the glycopeptide antibiotic scaffold by the sulfotransferase StaL

Shi, R., Munger, C., Kalan, L., Sulea, T., Wright, G.D., Cygler, M.

(2012) Proc Natl Acad Sci U S A

Macromolecule Content

Total Structure Weight: 65.55 kDa
Atom Count: 3,899
Modeled Residue Count: 502
Deposited Residue Count: 579
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
StaL	A, B	286	Streptomyces toyocaensis	Mutation(s): 0 Gene Names: stal EC: 2.8.2.36
UniProt
Find proteins for Q8KLM3 (Streptomyces toyocaensis) Explore Q8KLM3 Go to UniProtKB: Q8KLM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8KLM3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
desulfo-A47934	C	7	Streptomyces toyocaensis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A3P Query on A3P Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ADENOSINE-3'-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ WHTCPDAXWFLDIH-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0UZ Query on 0UZ	C	D-PEPTIDE LINKING	C₈ H₈ Cl N O₃		--
3FG Query on 3FG	C	L-PEPTIDE LINKING	C₈ H₉ N O₄		--
3MY Query on 3MY	C	D-PEPTIDE LINKING	C₉ H₁₀ Cl N O₃		TYR
GHP Query on GHP	C	D-PEPTIDE LINKING	C₈ H₉ N O₃		--
OMY Query on OMY	C	L-PEPTIDE LINKING	C₉ H₁₀ Cl N O₄		TYR

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000812 Query on PRD_000812	C	desulfo-A47934	Glycopeptide / Antibiotic		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.272 (Depositor), 0.267 (DCC)
R-Value Work: 0.223 (Depositor), 0.215 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.442	α = 90
b = 82.583	β = 90
c = 123.076	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-07-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-07-04
Type: Initial release
Version 1.1: 2012-12-12
Changes: Other
Version 1.2: 2017-11-15
Changes: Refinement description
Version 2.0: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Polymer sequence, Refinement description
Version 2.1: 2023-12-06
Changes: Data collection, Derived calculations

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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.