3LWF | pdb_00003lwf

Crystal structure of Putative transcriptional regulator (NP_470886.1) from LISTERIA INNOCUA at 2.06 A resolution

PDB DOI: https://doi.org/10.2210/pdb3LWF/pdb

Classification: Transcription regulator
Organism(s): Listeria innocua
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-23 Released: 2010-05-12
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Putative transcriptional regulator (NP_470886.1) from LISTERIA INNOCUA at 2.06 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 74.74 kDa
Atom Count: 5,000
Modeled Residue Count: 576
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator	A, B, C, D	159	Listeria innocua	Mutation(s): 0 Gene Names: lin1550
UniProt
Find proteins for Q92BJ8 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q92BJ8 Go to UniProtKB: Q92BJ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92BJ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain U [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain CA [auth D] SDF format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain U [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain U [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] CA [auth D] E [auth A] F [auth A] AA [auth D], BA [auth D], CA [auth D], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], T [auth C], U [auth C], V [auth C], W [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain X [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain M [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain X [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain X [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A]	DA [auth D] M [auth A] R [auth B] S [auth B] X [auth C] DA [auth D], M [auth A], R [auth B], S [auth B], X [auth C], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33LWF

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.961	α = 90
b = 115.782	β = 120.7
c = 75.927	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Data collection, Refinement description, Structure summary