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- PDB-3qmq: Crystal Structure of E. coli LsrG -

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Basic information

Entry
Database: PDB / ID: 3qmq
TitleCrystal Structure of E. coli LsrG
ComponentsAutoinducer-2 (AI-2) modifying protein LsrG
KeywordsISOMERASE / AI-2 modifying protein
Function / homology
Function and homology information


(4S)-4-hydroxy-5-phosphooxypentane-2,3-dione isomerase / intramolecular oxidoreductase activity, interconverting aldoses and ketoses / cytoplasm
Similarity search - Function
(4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsMiller, S.T. / Russell, C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Processing the Interspecies Quorum-sensing Signal Autoinducer-2 (AI-2): CHARACTERIZATION OF PHOSPHO-(S)-4,5-DIHYDROXY-2,3-PENTANEDIONE ISOMERIZATION BY LsrG PROTEIN.
Authors: Marques, J.C. / Lamosa, P. / Russell, C. / Ventura, R. / Maycock, C. / Semmelhack, M.F. / Miller, S.T. / Xavier, K.B.
History
DepositionFeb 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autoinducer-2 (AI-2) modifying protein LsrG
B: Autoinducer-2 (AI-2) modifying protein LsrG
C: Autoinducer-2 (AI-2) modifying protein LsrG
D: Autoinducer-2 (AI-2) modifying protein LsrG


Theoretical massNumber of molelcules
Total (without water)46,1884
Polymers46,1884
Non-polymers00
Water5,188288
1
A: Autoinducer-2 (AI-2) modifying protein LsrG
D: Autoinducer-2 (AI-2) modifying protein LsrG


Theoretical massNumber of molelcules
Total (without water)23,0942
Polymers23,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-16 kcal/mol
Surface area10320 Å2
MethodPISA
2
B: Autoinducer-2 (AI-2) modifying protein LsrG
C: Autoinducer-2 (AI-2) modifying protein LsrG


Theoretical massNumber of molelcules
Total (without water)23,0942
Polymers23,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-14 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.643, 83.397, 63.595
Angle α, β, γ (deg.)90.000, 89.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Autoinducer-2 (AI-2) modifying protein LsrG


Mass: 11547.111 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 MG1655 / Gene: G2583_1883, lsrG / Plasmid: pProEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3QT67
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.5
Details: 1.65 M NaCitrate, pH 6.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 42888 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.127 / Χ2: 1.269 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.863.60.4242840.504199.8
1.86-1.943.70.33242850.727199.8
1.94-2.033.70.28242700.962199.8
2.03-2.133.70.24342561.091199.8
2.13-2.273.70.20642851.272199.7
2.27-2.443.70.18342781.391199.8
2.44-2.693.70.16342941.504199.8
2.69-3.083.70.14242911.653199.8
3.08-3.883.60.1142991.76199.5
3.88-503.70.08643461.824198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.1
Highest resolutionLowest resolution
Rotation2.5 Å33.58 Å
Translation2.5 Å33.58 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.3phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry code 2GFF

2gff


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.294 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 2165 5.1 %RANDOM
Rwork0.2042 ---
obs0.2063 42865 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 58.05 Å2 / Biso mean: 23.609 Å2 / Biso min: 8.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å2-0 Å20.3 Å2
2---0.7 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 0 288 3508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223292
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9524442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91224.318176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44415590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8471520
X-RAY DIFFRACTIONr_chiral_restr0.1520.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212532
X-RAY DIFFRACTIONr_mcbond_it1.291.51958
X-RAY DIFFRACTIONr_mcangle_it2.13123182
X-RAY DIFFRACTIONr_scbond_it3.53931334
X-RAY DIFFRACTIONr_scangle_it5.6374.51260
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 149 -
Rwork0.281 2881 -
all-3030 -
obs--95.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38860.2230.23140.61220.22251.51280.0054-0.0528-0.0367-0.04470.0007-0.02430.1731-0.0457-0.00620.0288-0.00710.00020.01060.00730.01-9.5182-4.7975-28.1369
20.3868-0.1838-0.2690.85190.19780.85620.04040.03330.07290.03580.0242-0.0351-0.0285-0.0267-0.06470.01270.00030.00850.01340.00510.0143-8.5007-19.769-3.3763
31.16670.1385-0.19650.21910.10980.657-0.02190.00950.04490.05690.0280.00020.10130.0428-0.00610.02450.0091-0.00340.01650.01150.01368.7079-32.5924-9.0103
41.29970.1810.21490.1384-0.02310.683-0.0149-0.0521-0.058-0.05950.00870.0027-0.10650.07130.00620.0614-0.0149-0.00460.03670.01580.01037.42627.8428-22.5922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 96
2X-RAY DIFFRACTION1A97 - 288
3X-RAY DIFFRACTION2B0 - 96
4X-RAY DIFFRACTION2B97 - 285
5X-RAY DIFFRACTION3C-2 - 96
6X-RAY DIFFRACTION3C97 - 286
7X-RAY DIFFRACTION4D-2 - 96
8X-RAY DIFFRACTION4D97 - 287

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