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- PDB-6kjq: Functional and structural insights into the unusual oxyanion hole... -

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Basic information

Entry
Database: PDB / ID: 6kjq
TitleFunctional and structural insights into the unusual oxyanion hole-like geometry in macrolactin acyltransferase selective for dicarboxylic acyl donors
ComponentsPutative beta-lactamase
KeywordsTRANSFERASE / acyltransferase
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-D9F / Putative beta-lactamase
Similarity search - Component
Biological speciesJeotgalibacillus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsXiao, F. / Dong, S. / Feng, Y. / Li, W.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Structural Basis of Specificity for Carboxyl-Terminated Acyl Donors in a Bacterial Acyltransferase.
Authors: Xiao, F. / Dong, S. / Liu, Y. / Feng, Y. / Li, H. / Yun, C.H. / Cui, Q. / Li, W.
History
DepositionJul 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 22, 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: Putative beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5682
Polymers44,1651
Non-polymers4031
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.240, 116.240, 50.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

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Components

#1: Protein Putative beta-lactamase / MlnI


Mass: 44165.324 Da / Num. of mol.: 1 / Mutation: S73A, K76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jeotgalibacillus marinus (bacteria) / Gene: mlnI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1X4V6
#2: Chemical ChemComp-D9F / (3~{Z},5~{E},8~{S},9~{E},11~{E},14~{S},16~{R},17~{Z},19~{E},24~{R})-24-methyl-8,14,16-tris(oxidanyl)-1-oxacyclotetracosa-3,5,9,11,17,19-hexaen-2-one


Mass: 402.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 35.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.8 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→46.12 Å / Num. obs: 14362 / % possible obs: 96.6 % / Redundancy: 10.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.041 / Rrim(I) all: 0.135 / Net I/σ(I): 11.8 / Num. measured all: 148709 / Scaling rejects: 589
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.439.70.5191287413320.7960.1780.554.593.9
9.1-46.1210.90.07634363160.9960.0240.0822.599.5

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KJH

6kjh


Resolution: 2.35→42.873 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.65
RfactorNum. reflection% reflection
Rfree0.24 1433 10 %
Rwork0.1816 --
obs0.1874 14330 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.47 Å2 / Biso mean: 33.1205 Å2 / Biso min: 10.39 Å2
Refinement stepCycle: final / Resolution: 2.35→42.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2795 0 29 116 2940
Biso mean--44.9 32.43 -
Num. residues----359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3501-2.43410.35771350.2665121393
2.4341-2.53150.33031360.2321123293
2.5315-2.64670.32921370.2024122993
2.6467-2.78630.28481350.2038121293
2.7863-2.96080.26891380.1996124394
2.9608-3.18930.24011400.1951126697
3.1893-3.51020.24421480.1678132899
3.5102-4.01780.19461490.15881345100
4.0178-5.06070.1781530.14741373100
5.0607-42.8730.22971620.1791456100
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)
14.59992.5047-1.0097.9237-2.56175.07570.1556-0.40360.20350.5022-0.4009-0.9275-0.18450.67930.0970.18550.013-0.06140.2649-0.07240.372724.1783-32.984419.9807
24.06851.915-1.24325.7505-1.06444.67320.29280.1080.63580.2488-0.1302-0.3982-0.54210.2341-0.09670.22120.0129-0.02010.2103-0.03760.396919.4833-23.083518.1464
36.17920.58861.69770.71890.01671.7654-0.2482-0.08670.58130.07290.170.1461-0.17730.10720.08650.22460.0209-0.00610.0993-0.02320.25832.0576-24.02313.409
42.5753-1.2798-0.12843.343-0.01684.29340.11030.4050.3867-0.3351-0.1731-0.0853-0.2611-0.04040.04470.22140.0056-0.05180.22280.06340.2183-8.1964-26.5761-4.6592
53.0380.47550.88892.99140.07852.1099-0.09360.05440.6336-0.2588-0.01430.0263-0.56650.20260.08410.3594-0.02040.02530.16570.01250.34441.4425-14.400211.7982
62.69410.65750.08132.6794-0.1363.178-0.0159-0.0216-0.01240.11830.0389-0.01350.21370.06850.03670.08260.0333-0.03720.10850.01140.16960.2131-34.483611.6305
72.4029-0.7771.40774.506-0.71053.0822-0.00030.12150.0881-0.1881-0.0308-0.0899-0.0652-0.02460.02990.10370.02210.03640.1351-0.00790.224813.4148-36.031612.1506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 27 )A7 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 61 )A28 - 61
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 88 )A62 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 180 )A89 - 180
5X-RAY DIFFRACTION5chain 'A' and (resid 181 through 235 )A181 - 235
6X-RAY DIFFRACTION6chain 'A' and (resid 236 through 302 )A236 - 302
7X-RAY DIFFRACTION7chain 'A' and (resid 303 through 365 )A303 - 365

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