5BMO

LnmX protein, a putative GlcNAc-PI de-N-acetylase from Streptomyces atroolivaceus

PDB DOI: https://doi.org/10.2210/pdb5BMO/pdb

Classification: HYDROLASE
Organism(s): Streptomyces atroolivaceus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-05-22 Released: 2015-06-10
Deposition Author(s): Osipiuk, J., Hatzos-Skintges, C., Cuff, M., Endres, M., Babnigg, G., Lohman, J., Ma, M., Rudolf, J., Chang, C.-Y., Shen, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.215
R-Value Work: 0.168
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

LnmX protein, a putative GlcNAc-PI de-N-acetylase from Streptomyces atroolivaceus.

Osipiuk, J., Hatzos-Skintges, C., Cuff, M., Endres, M., Babnigg, G., Lohman, J., Ma, M., Rudolf, J., Chang, C.-Y., Shen, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

To be published.

Macromolecule Content

Total Structure Weight: 80.31 kDa
Atom Count: 5,916
Modelled Residue Count: 723
Deposited Residue Count: 738
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein LnmX	A, B, C	246	Streptomyces atroolivaceus	Mutation(s): 0 Gene Names: LnmX
UniProt
Find proteins for Q8GGM8 (Streptomyces atroolivaceus) Explore Q8GGM8 Go to UniProtKB: Q8GGM8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8GGM8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C]	E [auth A], G [auth B], I [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C]	D [auth A], F [auth B], H [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.215
R-Value Work: 0.168
R-Value Observed: 0.170
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.998	α = 90
b = 71.998	β = 90
c = 284.458	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-06-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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: 2015-06-10
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
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5BMO

LnmX protein, a putative GlcNAc-PI de-N-acetylase from Streptomyces atroolivaceus

LnmX protein, a putative GlcNAc-PI de-N-acetylase from Streptomyces atroolivaceus.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)