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- PDB-4p2v: Structure of the AI-2 processing enzyme LsrF in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 4p2v
TitleStructure of the AI-2 processing enzyme LsrF in complex with the product of the LsrG reaction P-HPD
ComponentsUncharacterized aldolase LsrF
KeywordsLYASE / Thiolase
Function / homology
Function and homology information


3-hydroxy-5-phosphooxypentane-2,4-dione thiolase / fructose-bisphosphate aldolase activity / acyltransferase activity, transferring groups other than amino-acyl groups / cytoplasm
Similarity search - Function
3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase / Aldolase FbaB-like, archaeal-type / : / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-26T / 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsMiller, S.T. / Oh, I.K. / Xavier, K.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM096478-01A1 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: LsrF, a coenzyme A-dependent thiolase, catalyzes the terminal step in processing the quorum sensing signal autoinducer-2.
Authors: Marques, J.C. / Oh, I.K. / Ly, D.C. / Lamosa, P. / Ventura, M.R. / Miller, S.T. / Xavier, K.B.
History
DepositionMar 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized aldolase LsrF
B: Uncharacterized aldolase LsrF
C: Uncharacterized aldolase LsrF
D: Uncharacterized aldolase LsrF
E: Uncharacterized aldolase LsrF
F: Uncharacterized aldolase LsrF
G: Uncharacterized aldolase LsrF
H: Uncharacterized aldolase LsrF
I: Uncharacterized aldolase LsrF
K: Uncharacterized aldolase LsrF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,27920
Polymers320,15810
Non-polymers2,12110
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53930 Å2
ΔGint-210 kcal/mol
Surface area84240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.617, 105.742, 170.402
Angle α, β, γ (deg.)90.00, 101.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized aldolase LsrF


Mass: 32015.766 Da / Num. of mol.: 10 / Mutation: K203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lsrF, yneB, b1517, JW1510 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P76143, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Chemical
ChemComp-26T / (3R)-3-hydroxy-2,4-dioxopentyl dihydrogen phosphate


Mass: 212.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C5H9O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 21% PEG 400, 110 mM MgCl2, 1 mM DTT, and 100 mM Tris pH 8.0 well solution. Drop was 1ul protein (7.3mg/ml) and 1 ul well solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.51→49.263 Å / Num. obs: 92529 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.32
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4909 / Mean I/σ(I) obs: 2.47 / % possible all: 97

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: DEV_1626) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GKF
Resolution: 2.51→49.26 Å / Cross valid method: FREE R-VALUE / σ(F): 1.68 / Phase error: 35.16 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.271 4695 5.07 %Random Selection
Rwork0.235 ---
obs0.237 92513 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21452 0 130 596 22178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721960
X-RAY DIFFRACTIONf_angle_d1.37129723
X-RAY DIFFRACTIONf_dihedral_angle_d14.4328155
X-RAY DIFFRACTIONf_chiral_restr0.0573339
X-RAY DIFFRACTIONf_plane_restr0.0073896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.55520.32951860.30564304X-RAY DIFFRACTION93
2.5552-2.60170.32522360.30114410X-RAY DIFFRACTION95
2.6017-2.65170.36572280.32144369X-RAY DIFFRACTION95
2.6517-2.70580.40262290.35974318X-RAY DIFFRACTION92
2.7058-2.76450.3491920.30294357X-RAY DIFFRACTION95
2.7645-2.82880.31572540.29084420X-RAY DIFFRACTION94
2.8288-2.89950.312380.28284380X-RAY DIFFRACTION95
2.8995-2.97780.30792400.27524398X-RAY DIFFRACTION95
2.9778-3.06530.33652730.27044377X-RAY DIFFRACTION94
3.0653-3.16410.30352130.25874427X-RAY DIFFRACTION95
3.1641-3.27710.28442420.24324433X-RAY DIFFRACTION95
3.2771-3.40810.2982230.24034420X-RAY DIFFRACTION95
3.4081-3.56290.28972150.24944313X-RAY DIFFRACTION93
3.5629-3.75040.29012230.23584353X-RAY DIFFRACTION93
3.7504-3.98480.26942050.2244357X-RAY DIFFRACTION93
3.9848-4.29150.23592500.19534398X-RAY DIFFRACTION94
4.2915-4.72160.19672370.18574413X-RAY DIFFRACTION94
4.7216-5.40090.22422400.19564436X-RAY DIFFRACTION95
5.4009-6.78960.23482210.22014459X-RAY DIFFRACTION95
6.7896-28.64770.22512400.17944535X-RAY DIFFRACTION94
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.12430.00610.03450.71790.27480.63320.01840.2132-0.50740.04490.1507-0.10220.1301-0.24270.26770.3035-0.18290.05530.2106-0.24970.7967-23.8183-51.2613-31.789
20.181-0.14260.14091.00550.01031.485-0.12260.4396-0.1891-0.01430.05350.07650.0932-0.31920.01190.3037-0.09380.02090.3944-0.21580.5217-34.3645-39.7851-38.8899
30.29850.2177-0.59710.6072-0.41961.18710.0760.1138-0.2852-0.06250.11760.21360.3061-0.2430.00740.3915-0.30450.04520.4199-0.2520.9203-39.8016-56.781-35.2737
41.17371.47861.67114.96663.52983.0341-0.0488-0.0474-0.0498-0.06680.00990.01440.1572-0.04110.06570.6794-0.22350.00230.3098-0.07411.1574-35.3083-68.0331-26.823
50.6913-0.14970.21250.5236-0.19990.6336-0.00490.15660.29030.0967-0.05540.02310.01080.06810.03990.20860.0134-0.01640.1984-0.02620.2723-19.11472.8824-28.8505
60.8861-0.4418-0.60161.28630.34211.0680.06310.03560.1241-0.0341-0.08340.3864-0.1117-0.1151-0.04740.24150-0.02260.2715-0.06710.3919-32.64741.4302-18.7202
70.556-0.37890.26190.4504-0.4521.30210.0660.1160.25360.0841-0.07050.0267-0.2357-0.0825-0.0510.30720.01870.01750.2259-0.11770.6289-27.090819.3018-21.1869
80.1266-0.14560.05330.34820.02910.4796-0.11510.51550.0136-0.02140.0034-0.0371-0.1969-0.1790.10740.2959-0.0171-0.05170.69610.05170.2017-20.1975-3.4736-60.8456
90.3442-0.3342-0.33852.5615-0.58921.03660.08920.16260.096-0.13070.13780.29140.0541-0.0824-0.13930.30360.0213-0.01920.58720.07160.1668-31.34482.7574-50.6758
100.2934-0.01640.0180.4151-0.37170.3333-0.00020.02670.0106-0.0825-0.13140.2911-0.1575-0.07970.07420.26020.0624-0.1090.96110.17120.3901-31.9847.8701-67.2642
110.1468-0.04760.36140.864-0.11620.9104-0.0450.55330.194-0.93910.09950.4681-0.1418-0.06970.04380.76560.0927-0.05050.9820.23350.5471-25.791111.3617-76.9517
120.3168-0.11790.05540.4270.00160.40410.16120.7027-0.3644-0.1524-0.06730.2774-0.1269-0.11060.19540.1993-0.1445-0.06350.9814-0.42680.3959-25.1884-34.6774-61.8869
130.05950.0925-0.25321.1666-0.27311.09380.0312-0.10140.19250.02870.05540.4347-0.0745-0.4631-0.01870.32810.0794-0.0290.8338-0.23370.4814-36.2434-27.6442-61.5404
140.0758-0.08980.04030.1272-0.04380.05160.02190.1115-0.3061-0.1208-0.00480.23920.3471-0.07750.03040.3723-0.1009-0.15641.2352-0.34420.4453-37.8387-31.4379-71.9621
150.3218-0.42680.44131.339-0.42082.467-0.12560.24220.0068-0.47010.12970.19790.0484-0.0626-0.0160.7028-0.0245-0.19131.1804-0.48840.8078-34.4859-46.6304-80.9748
161.4398-0.89740.00230.8405-0.1380.38120.0198-0.3392-0.25230.14310.1342-0.19070.12060.1381-0.08680.45050.00470.00710.2338-0.06130.462-2.0284-46.2378-6.3477
170.48440.0899-0.09130.5706-0.09230.3429-0.0164-0.1041-0.1540.00890.05120.15870.03560.0072-0.00750.2531-0.0042-0.00250.2291-0.01520.2084-25.4042-20.0497-13.7447
180.35760.16780.05082.0722-0.32491.9219-0.01040.0341-0.3080.2774-0.13790.4798-0.0002-0.51940.09580.3034-0.01940.08820.259-0.09330.661-34.5783-26.5015-15.7933
191.14590.1226-0.09990.91840.14830.98810.1365-0.0267-0.05530.0807-0.12140.3428-0.1009-0.09870.05480.2809-0.06520.06890.326-0.01930.4743-37.2164-34.6799-11.2874
200.3522-0.7803-0.16652.18560.6260.22540.2978-0.25420.05210.17540.08490.17130.0281-0.2108-0.09160.3884-0.02460.13420.2963-0.01980.3641-35.5029-28.15410.51
210.4793-0.06750.34011.5213-0.34560.8259-0.1506-0.30910.03240.5004-0.09560.0637-0.03030.04570.0660.4916-0.00690.10250.39230.01490.3332-29.7894-22.86976.7076
220.49540.18690.06990.8281-0.07660.3441-0.0212-0.0766-0.1698-0.04590.012-0.1884-0.0146-0.03970.05760.25780.0079-0.02390.1851-0.01280.2335-0.3907-23.4858-13.5027
230.466-0.04270.19550.6844-0.50761.00130.0955-0.0624-0.07470.1436-0.07420.0439-0.020.19730.05220.2747-0.0061-0.02340.1687-0.00950.325111.788-19.8893-3.5134
240.219-0.2169-0.02880.24560.11340.3399-0.07210.2644-0.2764-0.16160.04650.06020.0683-0.0341-0.01740.3229-0.09160.15360.7063-0.4860.2979-4.2461-40.0526-60.7997
250.1342-0.1271-0.24740.11270.16990.84750.0580.1807-0.1652-0.20680.0934-0.3280.17040.090.02970.4064-0.07510.27320.6262-0.58570.61827.4346-51.5987-59.751
260.38220.0135-0.33150.4944-0.20091.2705-0.18260.3099-0.1517-0.56260.1584-0.13030.09980.1606-0.03940.62910.1304-0.05851.1528-0.48340.77852.1797-50.9959-77.8866
270.2569-0.19250.24510.4611-0.03370.48870.01870.52660.1588-0.02950.0392-0.19050.1884-0.1733-0.04260.202-0.04660.05480.8373-0.02090.0939-0.2212-9.2331-61.5745
280.70820.4005-0.26680.87860.27610.4179-0.00940.61840.0247-0.3836-0.0473-0.2657-0.16830.04160.04630.4153-0.02530.07181.03150.0830.272311.2325-8.7828-73.3433
290.81320.0510.11680.4122-0.26290.8837-0.04490.03050.31240.0355-0.0408-0.1477-0.03940.04570.04950.1916-0.0373-0.00530.1735-0.00410.312.06731.1389-32.4087
302.71521.0333-0.65421.21010.20821.63410.05560.14050.10670.20230.1105-0.3554-0.03910.2779-0.02310.169-0.0064-0.020.39410.01620.334615.68922.924-42.3347
310.8383-0.1495-0.02250.6183-0.77611.2944-0.13740.13320.40320.18470.062-0.1546-0.21930.24960.04030.3659-0.0449-0.04550.2506-0.00180.670714.459316.1816-28.8394
320.41020.21060.10350.6235-0.00180.06210.02390.1578-0.57420.0414-0.12250.02050.1575-0.0625-0.03030.3262-0.0540.0311-0.0644-0.20890.8033-4.5082-48.8414-30.9294
330.3882-0.11120.16670.7552-0.07080.14970.15290.0446-0.53360.05910.0037-0.33330.14850.1812-0.00230.38980.0296-0.0931-0.1267-0.13031.09725.7958-58.1109-23.3616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 9 THROUGH 117 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 118 THROUGH 197 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 198 THROUGH 261 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 262 THROUGH 289 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 9 THROUGH 165 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 166 THROUGH 216 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 217 THROUGH 289 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 9 THROUGH 148 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 149 THROUGH 216 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 217 THROUGH 261 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 262 THROUGH 289 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 9 THROUGH 164 )
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 165 THROUGH 183 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 184 THROUGH 261 )
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 262 THROUGH 289 )
16X-RAY DIFFRACTION16CHAIN 'E' AND (RESID 9 THROUGH 28 )
17X-RAY DIFFRACTION17CHAIN 'E' AND (RESID 29 THROUGH 164 )
18X-RAY DIFFRACTION18CHAIN 'E' AND (RESID 165 THROUGH 183 )
19X-RAY DIFFRACTION19CHAIN 'E' AND (RESID 184 THROUGH 216 )
20X-RAY DIFFRACTION20CHAIN 'E' AND (RESID 217 THROUGH 244 )
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESID 245 THROUGH 289 )
22X-RAY DIFFRACTION22CHAIN 'F' AND (RESID 10 THROUGH 165 )
23X-RAY DIFFRACTION23CHAIN 'F' AND (RESID 166 THROUGH 289 )
24X-RAY DIFFRACTION24CHAIN 'G' AND (RESID 9 THROUGH 164 )
25X-RAY DIFFRACTION25CHAIN 'G' AND (RESID 165 THROUGH 245 )
26X-RAY DIFFRACTION26CHAIN 'G' AND (RESID 246 THROUGH 289 )
27X-RAY DIFFRACTION27CHAIN 'H' AND (RESID 9 THROUGH 166 )
28X-RAY DIFFRACTION28CHAIN 'H' AND (RESID 167 THROUGH 289 )
29X-RAY DIFFRACTION29CHAIN 'I' AND (RESID 9 THROUGH 165 )
30X-RAY DIFFRACTION30CHAIN 'I' AND (RESID 166 THROUGH 216 )
31X-RAY DIFFRACTION31CHAIN 'I' AND (RESID 217 THROUGH 289 )
32X-RAY DIFFRACTION32CHAIN 'K' AND (RESID 9 THROUGH 164 )
33X-RAY DIFFRACTION33CHAIN 'K' AND (RESID 165 THROUGH 289 )

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