1D0K

THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH TWO MURODIPEPTIDES (GLCNAC-MURNAC-L-ALA-D-GLU)

PDB DOI: https://doi.org/10.2210/pdb1D0K/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 1999-09-12 Released: 2000-03-06
Deposition Author(s): van Asselt, E.J., Kalk, K.H., Dijkstra, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.202
R-Value Work: 0.165
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 37.68 kDa
Atom Count: 3,010
Modelled Residue Count: 314
Deposited Residue Count: 322
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
35KD SOLUBLE LYTIC TRANSGLYCOSYLASE	A	322	Escherichia coli	Mutation(s): 2
UniProt
Find proteins for P41052 (Escherichia coli (strain K12)) Explore P41052 Go to UniProtKB: P41052
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41052
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid	B, C	2		N/A	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G99515FY GlyCosmos: G99515FY

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGL Query on DGL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A]	F [auth A], H [auth A]	D-GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-GSVOUGTGSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
ALA Query on ALA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A]	E [auth A], G [auth A]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain G [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.202
R-Value Work: 0.165
R-Value Observed: 0.168
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.379	α = 90
b = 67.825	β = 90
c = 98.94	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-03-06

Deposition Author(s):

van Asselt, E.J.

Kalk, K.H.

Dijkstra, B.W.

Revision History (Full details and data files)

Version 1.0: 2000-03-06
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-11-03
Changes: Database references, Structure summary
Version 2.2: 2024-02-07
Changes: Data collection

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1D0K

THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH TWO MURODIPEPTIDES (GLCNAC-MURNAC-L-ALA-D-GLU)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)