1JOE

Crystal Structure of Autoinducer-2 Production Protein (LuxS) from Heamophilus influenzae

PDB DOI: https://doi.org/10.2210/pdb1JOE/pdb

Classification: SIGNALING PROTEIN
Organism(s): Haemophilus influenzae Rd KW20
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2001-07-27 Released: 2001-08-08
Deposition Author(s): Chen, C.C.H., Parsons, J.F., Lim, K., Lehmann, C., Tempczyk, A., Eisenstein, E., Herzberg, O., Structure 2 Function Project (S2F)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.299 (Depositor), 0.260 (DCC)
R-Value Work:
0.205 (Depositor), 0.200 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF AUTOINDUCER-2 PRODUCTION PROTEIN (LUXS) FROM HEAMOPHILUS INFLUENZAE--A CASE OF TWINNED CRYSTAL

Chen, C.C.H., Parsons, J.F., Lim, K., Lehmann, C., Tempczyk, A., Eisenstein, E., Herzberg, O.

To be published.

Macromolecule Content

Total Structure Weight: 75.26 kDa
Atom Count: 4,722
Modelled Residue Count: 592
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AUTOINDUCER-2 PRODUCTION PROTEIN	A, B, C, D	167	Haemophilus influenzae Rd KW20	Mutation(s): 0 EC: 4.4.1.21
UniProt
Find proteins for P44007 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44007 Go to UniProtKB: P44007
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P44007
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.299 (Depositor), 0.260 (DCC)
R-Value Work: 0.205 (Depositor), 0.200 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.53	α = 90
b = 115.53	β = 90
c = 51.23	γ = 90

Software Package:

Software Name	Purpose
SHELXS	phasing
MLPHARE	phasing
DM	model building
SHELXL-97	refinement
X-GEN	data reduction
X-GEN	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2001-08-08

Deposition Author(s):

Structure 2 Function Project (S2F)

Revision History (Full details and data files)

Version 1.0: 2001-08-08
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2024-02-07
Changes: Data collection, Database references, Derived calculations