4XVO

L,D-transpeptidase from Mycobacterium smegmatis

PDB DOI: https://doi.org/10.2210/pdb4XVO/pdb

Classification: TRANSFERASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-01-27 Released: 2015-02-11
Deposition Author(s): Osipiuk, J., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.238
R-Value Work: 0.198
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

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

Literature

L,D-transpeptidase from Mycobacterium smegmatis

Osipiuk, J., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 72.18 kDa
Atom Count: 5,201
Modelled Residue Count: 651
Deposited Residue Count: 669
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase	A, B, C	223	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: MSMEI_3449
UniProt
Find proteins for I7G323 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore I7G323 Go to UniProtKB: I7G323
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7G323
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C]	D [auth A], E [auth A], F [auth B], G [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.238
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: C 2 2 2₁
Diffraction Data: https://doi.org/10.18430/M34XVO

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.39	α = 90
b = 160.047	β = 90
c = 209.912	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-02-11

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History (Full details and data files)

Version 1.0: 2015-02-11
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
Version 1.2: 2019-12-25
Changes: Author supporting evidence

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Help and Resources

4XVO

L,D-transpeptidase from Mycobacterium smegmatis

L,D-transpeptidase from Mycobacterium smegmatis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)