2HKL | pdb_00002hkl

Crystal structure of Enterococcus faecium L,D-transpeptidase C442S mutant

PDB DOI: https://doi.org/10.2210/pdb2HKL/pdb

Classification: TRANSFERASE
Organism(s): Enterococcus faecium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-07-05 Released: 2007-05-22
Deposition Author(s): Delfosse, V., Hugonnet, J.-E., Magnet, S., Mainardi, J.-L., Arthur, M., Mayer, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.249 (Depositor), 0.249 (DCC)
R-Value Work:
0.216 (Depositor), 0.210 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2HKL

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

Literature

Crystal structure of Enterococcus faecium L,D-transpeptidase C442S mutant

Delfosse, V., Hugonnet, J.-E., Magnet, S., Mainardi, J.-L., Arthur, M., Mayer, C.

To be published.

Macromolecule Content

Total Structure Weight: 83.93 kDa
Atom Count: 6,210
Modeled Residue Count: 744
Deposited Residue Count: 750
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-TRANSPEPTIDASE	A, B, C	250	Enterococcus faecium	Mutation(s): 1 Gene Names: ldtfm
UniProt
Find proteins for Q3Y185 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)) Explore Q3Y185 Go to UniProtKB: Q3Y185
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3Y185
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.249 (Depositor), 0.249 (DCC)
R-Value Work: 0.216 (Depositor), 0.210 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.14	α = 90
b = 132.66	β = 89.98
c = 70.12	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-05-22

Deposition Author(s):

Hugonnet, J.-E.

Mainardi, J.-L.

Revision History (Full details and data files)

Version 1.0: 2007-05-22
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-08-30
Changes: Data collection, Refinement description

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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.