6DFU | pdb_00006dfu

Tryptophan--tRNA ligase from Haemophilus influenzae.

PDB DOI: https://doi.org/10.2210/pdb6DFU/pdb

Classification: LIGASE
Organism(s): Haemophilus influenzae Rd KW20
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-05-15 Released: 2018-05-23
Deposition Author(s): Osipiuk, J., Maltseva, N., Mulligan, R., Grimshaw, S., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.238 (Depositor), 0.245 (DCC)
R-Value Work:
0.187 (Depositor), 0.194 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Tryptophan--tRNA ligase from Haemophilus influenzae.

Osipiuk, J., Maltseva, N., Mulligan, R., Grimshaw, S., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 75.84 kDa
Atom Count: 5,566
Modeled Residue Count: 663
Deposited Residue Count: 674
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan--tRNA ligase	A, B	337	Haemophilus influenzae Rd KW20	Mutation(s): 0 Gene Names: trpS, HI_0637 EC: 6.1.1.2
UniProt
Find proteins for P43835 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P43835 Go to UniProtKB: P43835
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43835
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRP Query on TRP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.238 (Depositor), 0.245 (DCC)
R-Value Work: 0.187 (Depositor), 0.194 (DCC)
R-Value Observed: 0.190 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.294	α = 90
b = 48.677	β = 101.13
c = 99.322	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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-23

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2018-05-23
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description