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

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Basic information

Entry
Database: PDB / ID: 4yfb
TitleStructure of N-acylhomoserine lactone acylase MacQ in complex with phenylacetic acid
Components(Protein related to penicillin ...) 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
2-PHENYLACETIC ACID / Protein related to penicillin acylase
Similarity search - Component
Biological speciesAcidovorax sp. MR-S7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 13, 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)338,90020
Polymers337,98712
Non-polymers9138
Water43,2542401
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)169,45010
Polymers168,9946
Non-polymers4564
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)169,45010
Polymers168,9946
Non-polymers4564
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.472, 139.026, 122.001
Angle α, β, γ (deg.)90.00, 111.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein related to penicillin ... , 3 types, 12 molecules ADGJBEHKCFIL

#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

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Non-polymers , 3 types, 2409 molecules

#4: Chemical
ChemComp-PAC / 2-PHENYLACETIC ACID


Mass: 136.148 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H8O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2401 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.42 Å3/Da / Density % sol: 49.2 %
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: 1.75→50 Å / Num. obs: 319483 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.29
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 3.18 / % possible all: 99.7

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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: PDB code, 2WYB

2wyb


Resolution: 1.75→25.14 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.815 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19344 16060 5 %RANDOM
Rwork0.16055 ---
obs0.16221 303343 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.298 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.44 Å2
2--0.33 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23038 0 64 2401 25503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01923794
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.93132401
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64853037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84323.0041092
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.249153414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91615196
X-RAY DIFFRACTIONr_chiral_restr0.1560.23449
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02118784
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 1206 -
Rwork0.25 21994 -
obs--99.48 %
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)
11.24460.62550.14941.45850.25940.9297-0.0217-0.1243-0.06090.0803-0.03130.05020.104-0.15240.05310.0184-0.01410.01590.0495-0.01110.021717.2616-0.481575.9524
23.43751.31730.61875.62911.03281.88260.03680.0513-0.38750.06420.0128-0.23570.40890.067-0.04960.14430.0213-0.01720.07310.02970.073928.6244-11.776481.0559
30.7774-0.0401-0.03211.46180.86621.6197-0.0051-0.1129-0.10.0259-0.06360.0420.1042-0.20940.06870.0303-0.03550.00450.0670.00240.040814.6892-3.925876.7004
49.03880.05290.01852.5548-4.02936.3869-0.13540.1441-0.7246-0.36920.1112-0.02270.5045-0.3410.02420.4684-0.0009-0.01610.503-0.13610.43326.6822-20.919745.0978
514.728113.330516.318412.117914.805818.10750.1038-0.2149-0.3901-0.3140.0452-0.2776-0.2698-0.2574-0.14890.8461-0.1117-0.17620.3799-0.05740.47717.5993-8.691253.9791
60.6442-0.0171-0.07440.88960.10010.7802-0.0304-0.0766-0.1460.0835-0.03290.02820.2057-0.02650.06330.0614-0.00470.01140.01430.00690.059725.9149-10.086564.9447
70.58210.1476-0.05221.6713-0.31780.877-0.01190.085-0.0954-0.0449-0.00480.02110.15920.02410.01680.04340.01520.00770.0276-0.02220.043233.1855-10.036649.9831
80.53780.02480.41470.25070.00241.46050.0010.03970.0708-0.04190.0063-0.0092-0.0958-0.1023-0.00730.0260.0099-0.00070.01940.00770.054720.353212.435949.0738
91.1258-0.6447-0.13991.6323-0.29680.6529-0.03490.0739-0.0562-0.1335-0.0533-0.11050.20.08820.08820.07090.01630.02290.03340.0130.0281-14.22781.408338.0115
101.5360.4412-0.1791.2637-0.51.4566-0.04360.1643-0.1683-0.1766-0.0201-0.02890.24970.02350.06370.10530.02460.00930.0362-0.01260.0247-16.4428-0.738732.2288
115.554-3.2464-0.83558.74560.3681.0092-0.0441-0.12130.02040.0327-0.0319-0.4340.27020.20080.0760.19340.06040.05470.05130.04490.0942-10.7967-16.514449.7219
1213.6556-0.01091.17515.36342.11418.1270.1696-0.1503-0.63190.7531-0.1707-0.3729-0.14090.40470.00110.4905-0.00610.04360.3353-0.00640.2987-4.6269-20.370267.4169
1311.8387-21.11924.769937.7013-8.51351.9265-0.8086-0.4082-0.38191.70570.8470.5977-0.3841-0.1251-0.03830.57710.0649-0.08110.50910.0050.4526-15.5155-7.631159.1569
140.54570.007-0.21660.8945-0.07250.6951-0.0670.0041-0.1435-0.0703-0.0088-0.00560.2572-0.0090.07590.1067-0.01190.01210.01110.01060.0563-25.3917-10.423352.5702
151.48680.26910.60280.2250.26731.0627-0.0363-0.20210.06570.05980.0154-0.0036-0.05080.0750.02090.0458-0.0038-0.00450.091-0.00940.0301-17.311611.373276.9881
161.0402-0.05330.14050.5379-0.42152.04630.01450.00410.0729-0.0116-0.0282-0.0281-0.08760.11440.01370.0089-0.0063-0.00590.00740.00560.0307-19.849116.063650.4786
171.0909-0.3247-0.21221.4689-0.26171.0631-0.02960.0069-0.0093-0.03530.035-0.1757-0.02980.2856-0.00540.02490.0154-0.00110.1762-0.01760.038659.756-30.08640.9104
181.3842-0.23481.1263.4-0.87478.08660.03250.09060.1142-0.08330.08930.2487-0.23-0.2296-0.12180.0370.0244-0.01490.08980.02810.075238.8401-18.7983-3.8199
191.1616-0.4245-0.29021.00260.42791.25420.00820.05790.1792-0.03880.0378-0.0454-0.24080.12-0.04610.0651-0.0251-0.00220.11510.02090.065451.7675-16.9984-1.1439
2016.09362.36665.150218.45230.231311.1345-0.2360.7221.0359-0.34320.05840.3393-0.6848-0.41810.17760.26910.0409-0.02990.2307-0.01190.343920.5778-2.347714.4689
2118.7854-16.88881.357415.1965-1.22330.09890.26970.3487-0.192-0.2249-0.26620.23160.0180.014-0.00350.2740.0318-0.00290.2385-0.01480.388933.2803-15.09914.0644
220.51570.0349-0.14230.89750.09060.66890.0641-0.02490.15480.0073-0.0212-0.0091-0.19480.1352-0.0430.074-0.01710.00850.1113-0.00550.084247.5731-13.017117.6474
231.89290.52310.20740.3004-0.08760.78420.0387-0.11950.02890.03480.01190.0713-0.0106-0.0434-0.05060.07620.0267-0.00930.05020.02430.040125.2775-35.335928.0759
241.21880.1632-0.51090.4466-0.11021.2716-0.04630.0551-0.1334-0.0410.0088-0.04450.14050.09550.03760.05710.04-0.01130.05640.0030.051745.8908-39.47111.476
250.92890.2876-0.05961.370.40021.05340.0257-0.096-0.0230.1341-0.03790.0274-0.08560.02960.01220.0406-0.0008-0.00330.03160.00510.00771.5173-25.96451.3681
261.6238-0.08710.1730.9322-0.65831.7194-0.0084-0.11810.0180.10630.00420.0735-0.1455-0.09120.00420.0340.01230.00070.0306-0.01820.0333-4.5916-24.65533.9214
274.51813.41141.76678.9023.08535.31470.1253-0.1215-0.08880.08060.0477-0.4905-0.37090.306-0.1730.1534-0.0318-0.00080.0348-0.00040.045211.3019-8.0026-3.7349
288.1662-5.20875.831620.68447.00910.81950.01740.27950.14720.2310.0904-0.5752-0.00160.3589-0.10780.3537-0.0973-0.09050.4836-0.04570.328128.5938-2.2598-12.134
2914.495418.19512.874725.55363.38140.5977-0.20010.0064-0.028-0.52010.115-0.9883-0.03140.05560.08510.2526-0.07880.03530.4634-0.01410.348816.7902-16.6507-13.3885
300.5606-0.0397-0.20540.9048-0.04120.70340.06480.06440.07820.0425-0.03450.0341-0.2029-0.0187-0.03040.06870.0176-0.00270.0361-0.00450.03783.7643-13.5511-16.1338
311.4952-0.0934-0.4360.24910.12360.5876-0.01210.0206-0.0925-0.0038-0.02950.0049-0.02470.03970.04160.02170.0058-0.02530.0152-0.01050.03819.5143-36.3155-20.9971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 96
2X-RAY DIFFRACTION2A97 - 115
3X-RAY DIFFRACTION3A116 - 178
4X-RAY DIFFRACTION4B8 - 14
5X-RAY DIFFRACTION5B15 - 22
6X-RAY DIFFRACTION6C1 - 210
7X-RAY DIFFRACTION7C211 - 337
8X-RAY DIFFRACTION8C338 - 575
9X-RAY DIFFRACTION9D11 - 95
10X-RAY DIFFRACTION10D96 - 159
11X-RAY DIFFRACTION11D160 - 178
12X-RAY DIFFRACTION12E8 - 15
13X-RAY DIFFRACTION13E16 - 21
14X-RAY DIFFRACTION14F1 - 303
15X-RAY DIFFRACTION15F304 - 460
16X-RAY DIFFRACTION16F461 - 575
17X-RAY DIFFRACTION17G8 - 60
18X-RAY DIFFRACTION18G61 - 83
19X-RAY DIFFRACTION19G84 - 178
20X-RAY DIFFRACTION20H8 - 13
21X-RAY DIFFRACTION21H14 - 22
22X-RAY DIFFRACTION22I1 - 297
23X-RAY DIFFRACTION23I298 - 456
24X-RAY DIFFRACTION24I457 - 575
25X-RAY DIFFRACTION25J12 - 96
26X-RAY DIFFRACTION26J97 - 158
27X-RAY DIFFRACTION27J159 - 178
28X-RAY DIFFRACTION28K8 - 14
29X-RAY DIFFRACTION29K15 - 23
30X-RAY DIFFRACTION30L1 - 300
31X-RAY DIFFRACTION31L301 - 574

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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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