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- PDB-7am0: GqqA- a novel type of quorum quenching acylases -

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Basic information

Entry
Database: PDB / ID: 7am0
TitleGqqA- a novel type of quorum quenching acylases
ComponentsPrephenate dehydratase
KeywordsHYDROLASE / Quorum Quenching / Acylase
Function / homology
Function and homology information


prephenate dehydratase / prephenate dehydratase activity / chorismate mutase activity / L-phenylalanine biosynthetic process
Similarity search - Function
Bifunctional P-protein, chorismate mutase/prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / ACT domain profile. / ACT domain / ACT-like domain
Similarity search - Domain/homology
PHENYLALANINE / prephenate dehydratase
Similarity search - Component
Biological speciesKomagataeibacter europaeus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWerner, N. / Betzel, C.
CitationJournal: Sci Rep / Year: 2021
Title: The Komagataeibacter europaeus GqqA is the prototype of a novel bifunctional N-Acyl-homoserine lactone acylase with prephenate dehydratase activity.
Authors: Werner, N. / Petersen, K. / Vollstedt, C. / Garcia, P.P. / Chow, J. / Ferrer, M. / Fernandez-Lopez, L. / Falke, S. / Perbandt, M. / Hinrichs, W. / Betzel, C. / Streit, W.R.
History
DepositionOct 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
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: Prephenate dehydratase
B: Prephenate dehydratase
C: Prephenate dehydratase
D: Prephenate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8448
Polymers122,1834
Non-polymers6614
Water1,02757
1
A: Prephenate dehydratase
B: Prephenate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4224
Polymers61,0922
Non-polymers3302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-28 kcal/mol
Surface area22990 Å2
MethodPISA
2
C: Prephenate dehydratase
D: Prephenate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4224
Polymers61,0922
Non-polymers3302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-26 kcal/mol
Surface area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.872, 65.760, 102.660
Angle α, β, γ (deg.)90.00, 104.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Prephenate dehydratase / GqqA


Mass: 30545.850 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataeibacter europaeus (bacteria) / Gene: pheA, KOEU_05990 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M0ELU2, prephenate dehydratase
#2: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M Sodium succinate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→49.35 Å / Num. obs: 34461 / % possible obs: 99.44 % / Redundancy: 6.8 % / CC1/2: 1 / Rrim(I) all: 0.04 / Net I/σ(I): 29.35
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.9 % / Num. unique obs: 3364 / CC1/2: 0.96 / Rrim(I) all: 0.52 / % possible all: 98.53

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Processing

Software
NameVersionClassification
PHENIX5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ALZ

7alz


Resolution: 2.5→49.35 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 35.138 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27735 2000 5.8 %RANDOM
Rwork0.23174 ---
obs0.23434 32460 99.78 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0.29 Å2
2--0.89 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8497 0 0 57 8554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0188691
X-RAY DIFFRACTIONr_bond_other_d0.0010.028118
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.88111813
X-RAY DIFFRACTIONr_angle_other_deg1.0432.93618718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02851101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.65122.595393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9141588
X-RAY DIFFRACTIONr_chiral_restr0.1160.21317
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029820
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021844
X-RAY DIFFRACTIONr_mcbond_it1.5873.4524431
X-RAY DIFFRACTIONr_mcbond_other1.5873.4524430
X-RAY DIFFRACTIONr_mcangle_it2.7155.1745523
X-RAY DIFFRACTIONr_mcangle_other2.7155.1745524
X-RAY DIFFRACTIONr_scbond_it1.3733.6134260
X-RAY DIFFRACTIONr_scbond_other1.3723.6124260
X-RAY DIFFRACTIONr_scangle_other2.3385.3626290
X-RAY DIFFRACTIONr_long_range_B_refined5.0441.3459090
X-RAY DIFFRACTIONr_long_range_B_other5.03541.3219086
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 144 -
Rwork0.307 2331 -
obs--98.61 %
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)
12.73220.50711.23661.32030.35131.7541-0.0703-0.03210.2002-0.0171-0.02190.02350.0635-0.0230.09220.28810.019-0.15280.57650.00420.093813.8128.272-1.188
21.77030.0898-0.1391.77980.46433.2125-0.01670.2521-0.1264-0.21220.1956-0.00450.07970.0418-0.17890.2405-0.0173-0.18010.5164-0.02160.163226.05512.826-6.449
30.6369-0.3345-0.08790.8381-0.83575.02340.0410.0202-0.0162-0.1572-0.1653-0.11190.05870.46150.12430.42990.0279-0.21280.8415-0.04890.171753.60716.65849.838
41.83110.54341.71431.46871.42656.05650.01110.19030.0158-0.1378-0.09120.0105-0.1539-0.26840.08020.38820.0934-0.19870.7701-0.00260.189437.14826.61856.201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 5:281 OR RESID 301:301 ) )A5 - 281
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 5:281 OR RESID 301:301 ) )A301
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 4:281 OR RESID 301:301 ) )B4 - 281
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 4:281 OR RESID 301:301 ) )B301
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 5:279 OR RESID 301:301 ) )C5 - 279
6X-RAY DIFFRACTION3( CHAIN C AND ( RESID 5:279 OR RESID 301:301 ) )C301
7X-RAY DIFFRACTION4( CHAIN D AND ( RESID 4:281 OR RESID 301:301 ) )D4 - 281
8X-RAY DIFFRACTION4( CHAIN D AND ( RESID 4:281 OR RESID 301:301 ) )D301

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