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- PDB-4yf9: Structure of N-acylhomoserine lactone acylase MacQ -

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Basic information

Entry
Database: PDB / ID: 4yf9
TitleStructure of N-acylhomoserine lactone acylase MacQ
Components(Protein related to penicillin acylase) x 3
KeywordsHYDROLASE / Acylase / Ntn-hydrolase fold
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 amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / 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 (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / 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 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile. / 4-Layer Sandwich / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein related to penicillin acylase
Similarity search - Component
Biological speciesAcidovorax sp. MR-S7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYasutake, Y. / Kusada, H. / Kimura, N.
CitationJournal: Sci Rep / Year: 2017
Title: Bifunctional quorum-quenching and antibiotic-acylase MacQ forms a 170-kDa capsule-shaped molecule containing spacer polypeptides
Authors: Yasutake, Y. / Kusada, H. / Ebuchi, T. / Hanada, S. / Kamagata, Y. / Tamura, T. / Kimura, N.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
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: Protein related to penicillin acylase
B: Protein related to penicillin acylase
C: Protein related to penicillin acylase
D: Protein related to penicillin acylase
E: Protein related to penicillin acylase
F: Protein related to penicillin acylase
G: Protein related to penicillin acylase
H: Protein related to penicillin acylase
I: Protein related to penicillin acylase
J: Protein related to penicillin acylase
K: Protein related to penicillin acylase
L: Protein related to penicillin acylase


Theoretical massNumber of molelcules
Total (without water)337,98712
Polymers337,98712
Non-polymers00
Water2,792155
1
A: Protein related to penicillin acylase
B: Protein related to penicillin acylase
C: Protein related to penicillin acylase
D: Protein related to penicillin acylase
E: Protein related to penicillin acylase
F: Protein related to penicillin acylase


Theoretical massNumber of molelcules
Total (without water)168,9946
Polymers168,9946
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Protein related to penicillin acylase
H: Protein related to penicillin acylase
I: Protein related to penicillin acylase
J: Protein related to penicillin acylase
K: Protein related to penicillin acylase
L: Protein related to penicillin acylase


Theoretical massNumber of molelcules
Total (without water)168,9946
Polymers168,9946
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.617, 90.113, 123.167
Angle α, β, γ (deg.)103.49, 104.96, 105.95
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein related to penicillin acylase / N-Acyl-L-homoserine lactone acylase / MacQ


Mass: 19231.340 Da / Num. of mol.: 4 / Fragment: alpha-chain, UNP residues 29-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidovorax sp. MR-S7 (bacteria) / Gene: AVS7_00617 / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1VBK6
#2: Protein/peptide
Protein related to penicillin acylase / N-Acyl-L-homoserine lactone acylase / MacQ


Mass: 2653.900 Da / Num. of mol.: 4 / Fragment: spacer peptide, UNP residues 207-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidovorax sp. MR-S7 (bacteria) / Gene: AVS7_00617 / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1VBK6
#3: Protein
Protein related to penicillin acylase / N-Acyl-L-homoserine lactone acylase / MacQ


Mass: 62611.613 Da / Num. of mol.: 4 / Fragment: beta-chain, UNP residues 234-806
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidovorax sp. MR-S7 (bacteria) / Gene: AVS7_00617 / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1VBK6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, calcium acetate, PEG 3350 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 98361 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.02
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.79 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WYB

2wyb


Resolution: 2.6→38.32 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 25.513 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 3.109 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24079 4943 5 %RANDOM
Rwork0.19591 ---
obs0.19818 93309 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.736 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å21.42 Å2-0.21 Å2
2---0.16 Å2-0.99 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23010 0 0 155 23165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01923614
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.92732163
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73453016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93422.9781088
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.835153397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.79715196
X-RAY DIFFRACTIONr_chiral_restr0.0770.23429
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118624
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 368 -
Rwork0.309 6826 -
obs--97.48 %
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)
11.81270.2337-0.38881.0704-0.35621.83410.06170.3381-0.0462-0.4992-0.04420.02630.34560.325-0.01750.44110.119-0.05850.1794-0.00780.0476-3.65795.5373-18.8227
20.8041-0.12970.63131.8251-0.17861.70210.15980.2677-0.12-0.3348-0.1833-0.14540.41560.58380.02350.35130.18460.06650.40330.00720.04989.43933.6506-14.8155
340.71366.13193.972714.079911.00958.63180.93270.47022.2347-0.3128-0.5138-0.5469-0.2609-0.3979-0.41890.6133-0.01730.07480.50320.2550.410125.80141.147114.811
40.0126-0.14610.25741.7115-3.02515.3543-0.0416-0.0548-0.0123-0.27560.5070.19920.5231-0.9595-0.46540.39260.1704-0.15590.6848-0.03410.63879.15110.12626.0242
50.4028-0.36030.28831.1844-0.32331.21060.15120.1411-0.1538-0.2733-0.1459-0.07990.44290.3626-0.00530.44070.1555-0.03030.2007-0.02260.12686.5939-9.7463-0.9805
60.80630.11220.58070.9251-0.13382.11190.0621-0.0514-0.0092-0.0126-0.01860.16330.09780.0962-0.04350.1209-0.00410.00210.0173-0.00630.0644-8.69279.021112.4674
71.3153-0.7614-0.28411.8485-0.03771.40030.0024-0.16920.08060.0601-0.001-0.17420.50590.1913-0.00140.22430.02270.01910.1938-0.0190.054224.935932.993623.7268
80.32240.17590.17541.6043-0.36830.67650.0359-0.070.0244-0.0285-0.0997-0.19320.46850.07110.06390.42780.06820.00770.2009-0.02240.043723.82227.818323.3817
923.9292-11.9522-1.522545.07779.80052.1939-0.2061-0.1097-1.2404-1.69910.08060.6453-0.32850.00070.12550.98550.20080.0880.67960.00340.094333.996812.3166-7.2035
103.6875-5.117110.56197.1038-14.660230.25630.13110.2702-0.0740.1647-0.12720.1059-0.30910.743-0.00390.7640.09740.06450.49470.01760.779529.927828.45131.3674
111.0262-0.2949-0.20710.6264-0.05071.2870.0392-0.01310.1044-0.0775-0.0753-0.20990.3020.33460.03610.14070.07780.0840.25360.0160.155436.454636.66796.3639
120.68670.2202-0.02720.65150.57761.75230.10260.19720.1758-0.1248-0.0379-0.02120.1537-0.1722-0.06470.14580.0310.04520.20050.06720.114312.92241.1057-4.4341
130.8564-0.5459-0.47091.5763-0.06022.2907-0.0816-0.0561-0.14130.13740.02360.14510.067-0.17220.0580.0621-0.07660.03240.1486-0.0250.19942.3968-41.20758.5948
141.056-0.07070.16832.1438-1.03021.8585-0.03990.0124-0.19020.23620.03280.4014-0.0157-0.28190.00710.0429-0.04950.06250.1878-0.04490.2311-5.5138-35.224959.3046
159.06464.047-3.49923.268421.001825.1961-0.7716-0.70360.3815-0.94941.13670.0635-0.60651.6838-0.36510.62270.17420.06360.58130.16210.1106-0.1667-2.56245.5374
160.45060.79180.73191.40581.29921.2025-0.2219-0.28230.4592-0.5236-0.52410.7418-0.4587-0.53990.7460.69810.24250.16330.6672-0.0690.87223.1314-20.900443.9727
170.9612-0.1172-0.32741.2878-0.04621.01460.00750.1773-0.0927-0.1289-0.00910.3165-0.0295-0.35320.00160.0406-0.0217-0.04960.2131-0.04890.1832-1.4413-29.640938.1697
181.0850.3574-0.36541.48780.02311.0390.0383-0.0603-0.0326-0.0568-0.0304-0.1107-0.00550.0814-0.0080.0111-0.01690.01190.0621-0.05250.127722.3505-31.175641.6577
191.62390.22520.01042.1516-0.55691.6495-0.0590.07740.12730.1310.1646-0.4795-0.3506-0.0985-0.10560.1192-0.0451-0.00030.1407-0.04980.258729.83745.302159.0967
203.21310.1819-1.6462.4397-0.08952.1919-0.13150.18190.03280.03440.2132-0.1367-0.3009-0.2097-0.08170.1238-0.0083-0.01030.1481-0.00960.123324.05523.340156.1922
2118.49281.3264.857710.17875.90014.3330.41540.7464-0.9530.2023-0.46560.41050.1935-0.11240.05030.4550.00430.12480.68710.18280.3691-2.8294-7.348370.6762
2245.28711.6492-8.73170.0658-0.32881.7204-1.0421-0.4262-2.3735-0.00660.2741-0.0780.1544-0.03990.7680.52110.1114-0.00540.7894-0.03740.554815.1293-5.717673.3897
231.79120.9831-2.48314.94872.87417.51390.1671-0.2634-0.18450.45420.4425-0.96250.02010.9702-0.60960.72510.0747-0.38420.1381-0.11180.388833.708-3.212292.0297
240.4470.1215-0.25662.1856-0.30770.9463-0.05880.02910.05730.59050.1485-0.2362-0.243-0.1286-0.08970.25760.0435-0.09150.1711-0.030.127821.8702-5.248777.685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 65
2X-RAY DIFFRACTION2A66 - 178
3X-RAY DIFFRACTION3B8 - 15
4X-RAY DIFFRACTION4B16 - 22
5X-RAY DIFFRACTION5C1 - 297
6X-RAY DIFFRACTION6C298 - 575
7X-RAY DIFFRACTION7D11 - 117
8X-RAY DIFFRACTION8D118 - 178
9X-RAY DIFFRACTION9E8 - 15
10X-RAY DIFFRACTION10E16 - 21
11X-RAY DIFFRACTION11F1 - 337
12X-RAY DIFFRACTION12F338 - 575
13X-RAY DIFFRACTION13G12 - 82
14X-RAY DIFFRACTION14G83 - 178
15X-RAY DIFFRACTION15H8 - 14
16X-RAY DIFFRACTION16H15 - 22
17X-RAY DIFFRACTION17I1 - 361
18X-RAY DIFFRACTION18I362 - 574
19X-RAY DIFFRACTION19J12 - 124
20X-RAY DIFFRACTION20J125 - 178
21X-RAY DIFFRACTION21K8 - 17
22X-RAY DIFFRACTION22K18 - 23
23X-RAY DIFFRACTION23L1 - 13
24X-RAY DIFFRACTION24L14 - 575

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