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- PDB-4yfa: Structure of N-acylhomoserine lactone acylase MacQ in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4yfa
TitleStructure of N-acylhomoserine lactone acylase MacQ in complex with decanoic acid
Components(Protein related to penicillin acylase) x 3
KeywordsHYDROLASE / Acylase / product complex / 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 Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / 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 Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / 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 / 4-Layer Sandwich / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
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: 2.2 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,67616
Polymers337,98712
Non-polymers6894
Water15,187843
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,3388
Polymers168,9946
Non-polymers3452
Water1086
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,3388
Polymers168,9946
Non-polymers3452
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.408, 89.851, 122.710
Angle α, β, γ (deg.)103.26, 104.84, 106.05
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: Chemical
ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H20O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.78 %
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: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 159207 / % possible obs: 98.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 23.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 2.3 / % possible all: 97.3

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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: 2.2→38.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 14.197 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23508 8025 5 %RANDOM
Rwork0.19349 ---
obs0.19559 151153 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.924 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å21.27 Å2-0.67 Å2
2---0.78 Å2-0.92 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23014 0 46 843 23903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01923662
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.92832208
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99953017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53922.9781088
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.539153397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.68615196
X-RAY DIFFRACTIONr_chiral_restr0.0820.23429
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118636
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: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 557 -
Rwork0.289 10704 -
obs--94.06 %
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)
11.6977-0.31830.11041.061-0.33991.13170.07150.23940.0527-0.4235-0.1265-0.02120.34990.52310.0550.41360.14430.01770.29620.03360.02153.14366.2454-15.0561
20.9398-0.2535-0.00781.9367-0.45091.07030.04840.3203-0.1459-0.5287-0.0395-0.04970.40450.405-0.0090.51880.19690.00030.3913-0.03310.04283.90712.6445-20.1567
39.9578-2.3353-0.11497.68130.14213.93620.52750.54670.85810.1723-0.455-0.4-0.0760.645-0.07260.39440.24520.07310.62750.12590.098522.64010.0138-3.1364
415.85553.4061-0.277212.70753.59315.2031-0.06740.53461.33880.2187-0.4752-0.2134-0.54850.80480.54260.4981-0.0018-0.00550.54720.15960.389624.141.035413.5565
523.423810.785521.45445.15869.216221.94720.7921-0.32490.30610.5478-0.47990.3426-0.05211.1618-0.31220.6952-0.14420.17871.2349-0.35870.30977.31551.59956.0476
60.8141-0.23530.13981.2663-0.3021.35050.12120.187-0.0312-0.2742-0.1599-0.15330.34710.49860.03870.40570.1817-0.00540.2624-0.01750.05569.862-3.8972-4.6006
71.0161-0.40340.40421.1567-0.36441.38780.16470.2192-0.1607-0.2196-0.1330.04920.46930.3105-0.03170.51220.1504-0.06010.154-0.03720.13133.2632-15.80792.6388
80.68530.05080.40030.869-0.15982.06520.0939-0.02920.0213-0.0164-0.01680.1820.07070.1017-0.07710.1566-0.00810.02350.0229-0.00870.0906-8.70179.016412.6977
91.434-0.7903-0.36712.6964-0.1620.6455-0.0158-0.1060.02610.1079-0.03180.02140.38850.04450.04760.3308-0.01390.05230.1294-0.00410.03720.824133.380622.9309
101.6187-0.1851.34256.42712.93712.9266-0.0951-0.02830.0120.53050.3317-0.48430.41940.4934-0.23660.28360.21810.02540.4427-0.02160.128536.467631.330425.4846
111.1889-0.1009-0.13741.00180.03211.1926-0.1107-0.05060.00160.1361-0.043-0.1190.58390.09030.15370.30270.04550.05270.15060.00460.073523.878128.125823.5315
1217.781-6.52452.592344.70794.481616.3604-0.2020.2705-1.1223-0.21890.3673-1.2286-0.0148-0.4131-0.16530.92290.0990.13240.60870.00130.271535.683810.0245-8.8707
130.4531-0.2718-1.74790.20470.93567.0591-0.349-0.0727-0.21310.22220.03190.31771.14690.23190.31710.69170.17240.05570.4717-0.02951.071929.663724.3262-0.6548
141.34930.6639-1.02391.2383-0.00573.52510.08260.01320.3174-0.0096-0.0518-0.02190.08040.2624-0.03080.01930.02420.04790.13770.03020.172826.229747.204411.0468
150.8913-0.2047-0.18020.8363-0.22751.19780.02710.01940.0547-0.0694-0.0618-0.1780.3510.31640.03470.14880.07460.06710.2750.02020.153839.280133.62574.9566
160.5290.07730.06640.65090.40451.76630.09920.18760.1633-0.1748-0.04720.03230.1423-0.2401-0.05190.123-0.01130.02370.26060.07650.13612.727141.0934-4.6635
170.9999-0.5036-0.5011.9392-0.06391.6489-0.0096-0.1236-0.14160.2373-0.01960.0626-0.0021-0.2220.02920.0717-0.06790.03090.1501-0.02010.20011.1222-38.284358.8835
181.9321-1.6452-1.7167.28681.45754.8778-0.10550.1618-0.29360.18850.02780.90540.1332-0.70430.07780.0576-0.11080.03190.3134-0.04350.4897-14.433-40.825653.3875
191.5217-0.77010.44562.3172-0.90961.8899-0.003-0.1012-0.10660.3472-0.05660.2217-0.0188-0.18650.05960.0837-0.07410.05070.1583-0.03090.2257-2.0665-35.371961.0401
2013.61870.53-1.816224.77898.140612.0468-0.3397-0.620.20010.83250.46430.1529-0.68070.5425-0.12460.2778-0.02160.00160.40560.05080.11950.1495-3.068845.3116
210.1089-0.9499-0.70458.75336.52054.86790.41960.20630.0168-0.0956-1.15070.3724-0.0764-1.06810.73110.52640.21370.30061.04050.22861.4284.7082-21.535744.0853
221.0681-0.2711-0.32821.4398-0.11921.1288-0.00390.1631-0.1114-0.0774-0.01750.2972-0.0622-0.37750.02140.0329-0.0095-0.03860.2037-0.06070.2499-3.4572-29.943238.8006
231.70170.32090.15361.45930.5131.63350.07810.07490.1457-0.20850.0267-0.1181-0.23290.1793-0.10480.0725-0.04750.07290.0897-0.04820.208328.5531-18.584233.3288
241.14090.1852-0.21841.07930.07651.518-0.0428-0.1466-0.25890.1221-0.0504-0.16270.17940.08660.09320.0444-0.01040.00780.072-0.01790.221717.2691-42.104347.3711
252.5219-0.36280.29851.9014-0.12011.5274-0.04430.1279-0.04850.05650.2413-0.5269-0.3135-0.1083-0.1970.1175-0.0439-0.00510.1562-0.03130.263929.57032.550258.4439
261.3963-0.1911-1.03133.35060.57222.3242-0.01920.14350.1737-0.12440.2455-0.5864-0.471-0.1153-0.22620.1714-0.04330.01020.1411-0.03530.315631.51938.65756.1089
279.1298-2.47565.26495.37280.19646.20950.07190.5581-0.25090.1870.22820.31360.1069-0.1703-0.30010.08020.05770.07450.32070.11630.11418.4424.289862.639
2858.7072-8.06252.35251.27-1.02413.1970.5292-1.5623-1.6512-0.00130.290.4473-0.26190.0727-0.81920.4934-0.17690.19360.67010.16370.5919-8.219-6.886270.8772
292.47450.9157-1.21060.3489-0.45870.6087-0.51730.7102-0.8766-0.17430.2554-0.2550.2794-0.37730.2620.6150.1718-0.16390.7752-0.02360.92779.8531-6.067671.7977
301.0713-0.01850.07981.76080.12061.2469-0.0252-0.01970.09790.47990.1714-0.0744-0.2557-0.2227-0.14620.26880.0416-0.02870.14530.0330.162617.32377.480975.4908
310.81780.44840.23673.4163-0.13921.2621-0.0635-0.0747-0.07471.05050.113-0.3841-0.0595-0.0804-0.04960.47360.0777-0.16710.1806-0.00720.1623.3749-22.031789.2007
320.8490.5166-0.36262.2857-0.44341.3325-0.1573-0.0244-0.00910.4240.2143-0.47940.08950.0123-0.0570.18860.0457-0.17020.1371-0.06330.246929.6007-16.17276.033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 95
2X-RAY DIFFRACTION2A96 - 164
3X-RAY DIFFRACTION3A165 - 178
4X-RAY DIFFRACTION4B8 - 17
5X-RAY DIFFRACTION5B18 - 23
6X-RAY DIFFRACTION6C1 - 152
7X-RAY DIFFRACTION7C153 - 297
8X-RAY DIFFRACTION8C298 - 574
9X-RAY DIFFRACTION9D11 - 88
10X-RAY DIFFRACTION10D89 - 115
11X-RAY DIFFRACTION11D116 - 178
12X-RAY DIFFRACTION12E8 - 12
13X-RAY DIFFRACTION13E13 - 22
14X-RAY DIFFRACTION14F1 - 74
15X-RAY DIFFRACTION15F75 - 337
16X-RAY DIFFRACTION16F338 - 574
17X-RAY DIFFRACTION17G12 - 93
18X-RAY DIFFRACTION18G94 - 115
19X-RAY DIFFRACTION19G116 - 178
20X-RAY DIFFRACTION20H8 - 15
21X-RAY DIFFRACTION21H16 - 23
22X-RAY DIFFRACTION22I1 - 337
23X-RAY DIFFRACTION23I338 - 457
24X-RAY DIFFRACTION24I458 - 574
25X-RAY DIFFRACTION25J12 - 95
26X-RAY DIFFRACTION26J96 - 159
27X-RAY DIFFRACTION27J160 - 178
28X-RAY DIFFRACTION28K8 - 12
29X-RAY DIFFRACTION29K13 - 23
30X-RAY DIFFRACTION30L1 - 297
31X-RAY DIFFRACTION31L298 - 389
32X-RAY DIFFRACTION32L390 - 575

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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