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- PDB-5c9i: Structure of N-acylhomoserine lactone acylase MacQ shortened spac... -

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Basic information

Entry
Database: PDB / ID: 5c9i
TitleStructure of N-acylhomoserine lactone acylase MacQ shortened spacer mutant (delta202-208) in uncleaved form
ComponentsProtein related to penicillin acylase
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/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
Protein related to penicillin acylase
Similarity search - Component
Biological speciesAcidovorax sp. MR-S7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 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
DepositionJun 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,4895
Polymers335,3974
Non-polymers921
Water42,6052365
1
C: Protein related to penicillin acylase
D: Protein related to penicillin acylase


Theoretical massNumber of molelcules
Total (without water)167,6982
Polymers167,6982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein related to penicillin acylase
B: Protein related to penicillin acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,7913
Polymers167,6982
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-13 kcal/mol
Surface area49840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.722, 137.769, 121.518
Angle α, β, γ (deg.)90.00, 111.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein related to penicillin acylase


Mass: 83849.203 Da / Num. of mol.: 4 / Fragment: UNP residues 36-806 / Mutation: deletion of residues 202-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidovorax sp. MR-S7 (bacteria) / Gene: AVS7_00617 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2 (DE3) / References: UniProt: A0A0A1VBK6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2365 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 6% Tacsimate pH 6.0, 14-16% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 290370 / % possible obs: 100 % / Redundancy: 3.8 % / Rsym value: 0.117 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.796 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20582 14559 5 %RANDOM
Rwork0.16587 ---
obs0.16789 275722 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.318 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å20.18 Å2
2--0.47 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22973 0 6 2365 25344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01923645
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.92632224
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00853038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9423.1381093
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.078153405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.82415190
X-RAY DIFFRACTIONr_chiral_restr0.1430.23433
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02118680
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: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 1070 -
Rwork0.265 19801 -
obs--98.41 %
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)
10.6360.31140.10681.32750.42540.451-0.0177-0.0971-0.07750.0788-0.00570.01820.0994-0.05660.02350.0259-0.00140.01220.04940.0170.014916.5741-3.363975.8913
20.88140.45290.45640.2470.22650.2433-0.20270.04970.251-0.04340.0790.1475-0.1178-0.03130.12370.4781-0.00540.01780.49150.04890.56174.4834-15.549758.1456
30.57330.1352-0.03490.83150.08630.4002-0.0252-0.0315-0.08910.02290.01950.00270.10050.01970.00570.02890.00740.00020.01290.00870.022126.8123-12.619160.2527
40.5789-0.03650.43840.1673-0.00611.36290.00110.02390.0365-0.03460.0038-0.0168-0.0146-0.0359-0.0050.0074-0.00060.00230.00450.00630.03721.528911.850847.692
50.6643-0.3411-0.03771.2726-0.33220.4651-0.0080.0887-0.0982-0.0541-0.0282-0.01930.08720.00750.03620.0231-0.00690.0040.0235-0.01070.02-15.0599-2.223836.5343
62.23532.27-1.30972.5467-2.03743.02420.2283-0.18320.10470.3426-0.1650.0166-0.4964-0.0099-0.06330.34910.0607-0.00440.40990.03020.41063.1861-14.152948.857
70.4953-0.2197-0.20170.84980.0640.4358-0.07030.0068-0.09260.00980.02120.0080.1267-0.03150.04910.0429-0.01470.00980.00830.00330.0316-25.8809-10.93352.006
80.6139-0.02960.22510.2321-0.00061.14440.0067-0.06430.03830.0403-0.00410.0026-0.04610.0608-0.00260.0097-0.00590.00340.0139-0.00380.0265-19.318512.918764.7751
90.8109-0.2963-0.06881.34140.11650.9980.00930.17750.1332-0.05460.0073-0.0118-0.161-0.0417-0.01660.0356-0.0022-0.00120.14320.02590.032252.6734-20.48330.2005
100.7627-0.053-0.1250.93080.18840.88570.05240.09290.1959-0.1016-0.0229-0.0245-0.2119-0.0248-0.02950.05660.00390.00820.06750.02570.074549.1868-13.579715.4189
114.759-2.5341.55052.5779-0.23433.27270.1117-0.06810.1712-0.1618-0.07860.0742-0.2493-0.3376-0.03310.18240.00940.04570.0483-0.00050.152945.016-0.180722.8443
120.82830.1896-0.080.2729-0.06290.42430.00980.0416-0.0166-0.01020.01270.0190.0295-0.0531-0.02250.02970.004-0.01710.03610.00520.01336.3268-34.605722.9438
130.93830.2675-0.08281.213-0.03270.97890.0644-0.15710.09840.0706-0.04780.0059-0.18480.1225-0.01650.0575-0.02610.00480.0609-0.01560.01140.9794-22.94851.8984
140.70470.0769-0.21890.8068-0.19651.00140.0788-0.02440.1650.0779-0.01490.0303-0.25880.0594-0.06390.0757-0.00820.01650.0118-0.01220.0434.121-13.3844-15.9893
151.3843-0.1207-0.36880.09240.04370.42380-0.0621-0.07630.0023-0.0171-0.0245-0.00650.09410.0170.0341-0.0015-0.01380.02870.01190.020921.0854-36.0617-20.9182
164.67-3.7079-5.459928.389917.14414.6929-0.068-0.30410.01980.3538-0.30040.7015-0.0229-0.29620.36840.09930.012-0.02270.14920.01810.0662-13.8848-38.27534.0868
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 180
2X-RAY DIFFRACTION2A181 - 201
3X-RAY DIFFRACTION3A202 - 507
4X-RAY DIFFRACTION4A508 - 777
5X-RAY DIFFRACTION5B11 - 180
6X-RAY DIFFRACTION6B181 - 199
7X-RAY DIFFRACTION7B200 - 505
8X-RAY DIFFRACTION8B506 - 777
9X-RAY DIFFRACTION9C8 - 201
10X-RAY DIFFRACTION10C202 - 429
11X-RAY DIFFRACTION11C430 - 463
12X-RAY DIFFRACTION12C464 - 777
13X-RAY DIFFRACTION13D12 - 201
14X-RAY DIFFRACTION14D202 - 504
15X-RAY DIFFRACTION15D505 - 768
16X-RAY DIFFRACTION16D769 - 777

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