5X7L | pdb_00005x7l

Structure of TsrD from Streptomyces laurentii

PDB DOI: https://doi.org/10.2210/pdb5X7L/pdb

Classification: ISOMERASE
Organism(s): Streptomyces laurentii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-02-27 Released: 2018-03-07
Deposition Author(s): Song, Y., Lin, Z., Deng, W., Liu, W.
Funding Organization(s): NSFC, STCSM, CAS

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free:
0.166 (Depositor), 0.178 (DCC)
R-Value Work:
0.151 (Depositor), 0.159 (DCC)
R-Value Observed:
0.151 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5X7L

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

Literature

Structure of TsrD from Streptomyces laurentii

Song, Y., Lin, Z., Deng, W., Liu, W.

To be published.

Macromolecule Content

Total Structure Weight: 31.52 kDa
Atom Count: 2,451
Modeled Residue Count: 269
Deposited Residue Count: 276
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TsrD	A, B	138	Streptomyces laurentii	Mutation(s): 0 Gene Names: tsrD
UniProt
Find proteins for C0JRY3 (Streptomyces laurentii) Explore C0JRY3 Go to UniProtKB: C0JRY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C0JRY3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free: 0.166 (Depositor), 0.178 (DCC)
R-Value Work: 0.151 (Depositor), 0.159 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.232	α = 90
b = 54.232	β = 90
c = 199.952	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data processing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Funding Organization	Location	Grant Number
NSFC	China	31430005, 21520102004, 21472231 and 21621002
STCSM	China	14JC1407700 and 15JC1400400
CAS	China	XDB20020200

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

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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.