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- PDB-1tm2: Crystal Structure of the apo form of the Salmonella typhimurium A... -

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Basic information

Entry
Database: PDB / ID: 1tm2
TitleCrystal Structure of the apo form of the Salmonella typhimurium AI-2 receptor LsrB
Componentssugar transport protein
KeywordsSIGNALING PROTEIN / PERIPLASMIC BINDING PROTEIN
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function
Autoinducer 2 ABC transporter, substrate-binding protein LsrB / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Autoinducer 2-binding protein LsrB / Autoinducer 2-binding protein LsrB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsMiller, S.T. / Xavier, K.B. / Campagna, S.R. / Taga, M.E. / Semmelhack, M.F. / Bassler, B.L. / Hughson, F.M.
CitationJournal: Mol.Cell / Year: 2004
Title: Salmonella typhimurium Recognizes a Chemically Distinct Form of the Bacterial Quorum-Sensing Signal AI-2
Authors: Miller, S.T. / Xavier, K.B. / Campagna, S.R. / Taga, M.E. / Semmelhack, M.F. / Bassler, B.L. / Hughson, F.M.
History
DepositionJun 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sugar transport protein


Theoretical massNumber of molelcules
Total (without water)34,2511
Polymers34,2511
Non-polymers00
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.984, 73.979, 116.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein sugar transport protein


Mass: 34250.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: LsrB / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8Z2X8, UniProt: Q8ZKQ1*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU200H11.5418
SYNCHROTRONNSLS X2520.9789, 0.9793, 0.9500
Detector
TypeIDDetector
RIGAKU RAXIS IV1IMAGE PLATE
ADSC QUANTUM 42CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSSINGLE WAVELENGTHMx-ray1
2Si111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97891
30.97931
40.951
ReflectionResolution: 1.9→27.13 Å / Num. all: 25812 / Num. obs: 25812 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2.02 Å / % possible all: 93.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→27.13 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2546 -RANDOM
Rwork0.191 ---
all0.193 25812 --
obs0.193 25812 97 %-
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 0 348 2750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.257 380 -
Rwork0.211 --
obs-4051 93.7 %

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