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- PDB-8so5: Crystal structure of the engineered quorum quenching acylase MacQ... -

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Basic information

Entry
Database: PDB / ID: 8so5
TitleCrystal structure of the engineered quorum quenching acylase MacQ variant M1 - acylated form
Components(Protein related to penicillin acylase) x 2
KeywordsHYDROLASE / n-terminal hydrolase / acylase / N-acyl-L-homoserine lactone
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process
Similarity search - Function
Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Nucleophile aminohydrolases, N-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
DECANOIC ACID / Protein related to penicillin acylase
Similarity search - Component
Biological speciesAcidovorax sp. MR-S7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSompiyachoke, K. / Elias, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133487 United States
CitationJournal: Protein Sci. / Year: 2024
Title: Engineering quorum quenching acylases with improved kinetic and biochemical properties.
Authors: Sompiyachoke, K. / Elias, M.H.
History
DepositionApr 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Protein related to penicillin acylase
I: Protein related to penicillin acylase
J: Protein related to penicillin acylase
L: Protein related to penicillin acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,7286
Polymers168,3834
Non-polymers3452
Water10,305572
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.070, 80.650, 101.600
Angle α, β, γ (deg.)90.00, 90.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein related to penicillin acylase


Mass: 22155.555 Da / Num. of mol.: 2 / Fragment: residues 25-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidovorax sp. MR-S7 (bacteria) / Gene: AVS7_00617 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1VBK6
#2: Protein Protein related to penicillin acylase


Mass: 62036.113 Da / Num. of mol.: 2 / Fragment: residues 234-806
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidovorax sp. MR-S7 (bacteria) / Gene: AVS7_00617 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1VBK6
#3: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl, 100 mM calcium acetate, 14-18% PEG 3350
PH range: 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.35→53.16 Å / Num. obs: 64842 / % possible obs: 98.9 % / Redundancy: 3.1 % / CC1/2: 0.994 / Net I/σ(I): 11.76
Reflection shellResolution: 2.35→2.45 Å / Num. unique obs: 7609 / CC1/2: 0.811 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→53.16 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.16 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22811 3243 5 %RANDOM
Rwork0.18521 ---
obs0.18734 61599 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.977 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.35→53.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11369 0 0 572 11941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.01111677
X-RAY DIFFRACTIONr_bond_other_d00.01610606
X-RAY DIFFRACTIONr_angle_refined_deg0.5611.64615918
X-RAY DIFFRACTIONr_angle_other_deg0.1961.56524281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70951483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.987594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87101668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0290.21695
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214245
X-RAY DIFFRACTIONr_gen_planes_other00.022951
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2412.945944
X-RAY DIFFRACTIONr_mcbond_other2.2412.945944
X-RAY DIFFRACTIONr_mcangle_it3.4855.2757423
X-RAY DIFFRACTIONr_mcangle_other3.4855.2767424
X-RAY DIFFRACTIONr_scbond_it2.7023.1445733
X-RAY DIFFRACTIONr_scbond_other2.7023.1445734
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3685.6648496
X-RAY DIFFRACTIONr_long_range_B_refined6.52127.4913515
X-RAY DIFFRACTIONr_long_range_B_other6.51527.3413444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 240 -
Rwork0.274 4555 -
obs--99.28 %

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