5H91 | pdb_00005h91

LbDERA mutant-T29L/F163Y

PDB DOI: https://doi.org/10.2210/pdb5H91/pdb

Classification: LYASE
Organism(s): Levilactobacillus brevis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-12-25 Released: 2016-12-28
Deposition Author(s): Jiao, X.-C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.175 (Depositor), 0.178 (DCC)
R-Value Work:
0.159 (Depositor), 0.161 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5H91

This is version 1.1 of the entry. See complete history.

Literature

Structure of 2-deoxyribose-5-phosphate aldolase LbDERAT29L/F163Y at 1.77 Angstroms resolution

Jiao, X.-C.

To be published.

Macromolecule Content

Total Structure Weight: 56.28 kDa
Atom Count: 3,787
Modeled Residue Count: 434
Deposited Residue Count: 530
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribose-phosphate aldolase	A, B	265	Levilactobacillus brevis	Mutation(s): 2 Gene Names: LbDm2_0848 EC: 4.1.2.4
UniProt
Find proteins for Q03Q50 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947)) Explore Q03Q50 Go to UniProtKB: Q03Q50
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03Q50
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B], D [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.175 (Depositor), 0.178 (DCC)
R-Value Work: 0.159 (Depositor), 0.161 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.381	α = 90
b = 97.381	β = 90
c = 119.921	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data processing
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-12-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-12-28
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references

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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.