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- PDB-4zo3: AidC, a Dizinc Quorum-Quenching Lactonase, in complex with a prod... -

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Basic information

Entry
Database: PDB / ID: 4zo3
TitleAidC, a Dizinc Quorum-Quenching Lactonase, in complex with a product N-hexnoyl-L-homoserine
ComponentsAcylhomoserine lactonase
KeywordsHYDROLASE / Quorum-quenching / N-acyl-L-homoserine / lactonase / dizinc / AidC
Function / homology
Function and homology information


carboxylic ester hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-hexanoyl-L-homoserine / Acylhomoserine lactonase
Similarity search - Component
Biological speciesChryseobacterium sp. StRB126 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMascarenhas, R. / Thomas, P.W. / Wu, C.-X. / Nocek, B.P. / Hoang, Q. / Fast, W. / Liu, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1308672 United States
Robert A. Welch FoundationF-1572 United States
Loyola University Chicago United States
CitationJournal: Biochemistry / Year: 2015
Title: Structural and Biochemical Characterization of AidC, a Quorum-Quenching Lactonase with Atypical Selectivity.
Authors: Mascarenhas, R. / Thomas, P.W. / Wu, C.X. / Nocek, B.P. / Hoang, Q.Q. / Liu, D. / Fast, W.
History
DepositionMay 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylhomoserine lactonase
B: Acylhomoserine lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9028
Polymers66,2062
Non-polymers6966
Water10,539585
1
A: Acylhomoserine lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4514
Polymers33,1031
Non-polymers3483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acylhomoserine lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4514
Polymers33,1031
Non-polymers3483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-17 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.090, 47.870, 249.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acylhomoserine lactonase / N-acylhomoserine lactonase / AidC


Mass: 33103.082 Da / Num. of mol.: 2 / Fragment: UNP residues 37-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chryseobacterium sp. StRB126 (bacteria)
Gene: aidC, CHSO_3121 / Plasmid: pMAL-C5X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I7HB71
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-C6L / N-hexanoyl-L-homoserine


Mass: 217.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H19NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MgCl2.6H2O (0.2 M), Bis-Tris (0.1 M), pH 6.5, 25 % (w/v) PEG 3350
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.67→34.521 Å / Num. obs: 66783 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 19.41 Å2 / Rpim(I) all: 0.076 / Rrim(I) all: 0.184 / Rsym value: 0.166 / Net I/av σ(I): 3.184 / Net I/σ(I): 6.7 / Num. measured all: 364755
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.67-1.763.10.80.43000695780.8581.2971.499.7
1.76-1.874.70.9660.64317191080.5020.9662.6100
1.87-25.60.6440.94779485600.3010.6444.1100
2-2.166.30.4571.35050680030.1980.4575.8100
2.16-2.366.10.3351.84535173820.1470.3357100
2.36-2.6460.2462.54024267160.1090.2468100
2.64-3.0560.1663.93588959680.0740.1669.9100
3.05-3.736.10.1085.83133751080.0470.10813100
3.73-5.286.60.0797.72652840220.0330.07915.7100
5.28-34.52160.0775.31393123380.0360.07713.799.3

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZO2

4zo2


Resolution: 1.67→34.521 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 3369 5.07 %
Rwork0.1844 63041 -
obs0.1865 66410 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.14 Å2 / Biso mean: 28.2405 Å2 / Biso min: 9.26 Å2
Refinement stepCycle: final / Resolution: 1.67→34.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4676 0 34 585 5295
Biso mean--40.34 36.63 -
Num. residues----588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184895
X-RAY DIFFRACTIONf_angle_d1.1646600
X-RAY DIFFRACTIONf_chiral_restr0.05735
X-RAY DIFFRACTIONf_plane_restr0.006841
X-RAY DIFFRACTIONf_dihedral_angle_d14.071780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.69390.3561210.29452452X-RAY DIFFRACTION94
1.6939-1.71910.32891450.29392529X-RAY DIFFRACTION97
1.7191-1.7460.29361410.26732569X-RAY DIFFRACTION99
1.746-1.77460.29531260.27622616X-RAY DIFFRACTION100
1.7746-1.80520.33411500.2612557X-RAY DIFFRACTION100
1.8052-1.83810.29141670.25192578X-RAY DIFFRACTION100
1.8381-1.87340.27581340.24072591X-RAY DIFFRACTION100
1.8734-1.91160.26171590.22432610X-RAY DIFFRACTION100
1.9116-1.95320.25151420.21762573X-RAY DIFFRACTION100
1.9532-1.99860.26371300.21472618X-RAY DIFFRACTION100
1.9986-2.04860.24711720.2122605X-RAY DIFFRACTION100
2.0486-2.1040.26431450.19962584X-RAY DIFFRACTION100
2.104-2.16590.2421380.19622657X-RAY DIFFRACTION100
2.1659-2.23580.20181260.19842628X-RAY DIFFRACTION100
2.2358-2.31570.23761450.19192606X-RAY DIFFRACTION100
2.3157-2.40840.25941340.18462628X-RAY DIFFRACTION100
2.4084-2.5180.22521450.19082639X-RAY DIFFRACTION100
2.518-2.65070.2441310.1912652X-RAY DIFFRACTION100
2.6507-2.81670.23051440.19092662X-RAY DIFFRACTION100
2.8167-3.0340.2051300.17832654X-RAY DIFFRACTION100
3.034-3.33910.20841360.16682694X-RAY DIFFRACTION100
3.3391-3.82180.19411530.15242673X-RAY DIFFRACTION100
3.8218-4.81290.16391300.13152773X-RAY DIFFRACTION100
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)
10.6728-0.1624-0.0520.54530.1140.5754-0.0065-0.09450.2201-0.0022-0.0262-0.1268-0.0628-0.0140.03090.125-0.0027-0.01510.091-0.02820.202414.5403-4.0677-45.0946
21.1452-0.16720.19790.3702-0.06760.41930.03360.14610.1197-0.1696-0.0971-0.0593-0.0866-0.02530.06440.19090.04730.01150.16670.01310.162812.7937-7.9401-62.3732
34.1467-2.82231.19833.6871-1.00660.63590.002-0.0090.30780.03280.0634-0.0212-0.2199-0.1308-0.04450.26130.09040.07940.25930.11390.214113.4771-1.3792-65.6931
40.5319-0.04270.26130.40210.04570.6527-0.0076-0.13170.00330.0267-0.02980.02070.1055-0.20290.04570.1411-0.02430.00630.1405-0.02120.12095.6725-13.5175-45.6769
50.6115-0.1774-0.00150.45880.18630.5101-0.121-0.20070.12720.07090.1159-0.05870.1141-0.1546-0.00140.23930.0027-0.01540.3562-0.12960.22311.25-7.4943-20.8292
60.18480.08830.0920.23830.11560.27-0.0393-0.20640.14170.1048-0.0065-0.0467-0.0646-0.0765-0.08960.24880.0407-0.08510.497-0.2840.367923.09251.8025-10.8801
70.37140.6714-0.65762.1061-1.67511.5440.05890.0002-0.10410.0706-0.0126-0.13340.0741-0.0067-0.04350.3448-0.0066-0.1160.6185-0.20190.335122.533-5.27691.548
80.06240.12010.00520.39220.10950.06080.0077-0.06470.07210.1085-0.0069-0.0445-0.09530.00860.03840.32830.0592-0.09410.4692-0.32320.459615.486912.9689-12.0762
90.0976-0.0207-0.14630.05680.0820.2665-0.0363-0.17550.09770.0665-0.00890.03990.025-0.12350.06580.22020.0432-0.0310.4574-0.23270.27723.7430.9056-18.2615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 154 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 194 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 211 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 330 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 37 through 90 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 194 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 195 through 211 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 212 through 259 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 260 through 330 )B0

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