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

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Basic information

Entry
Database: PDB / ID: 6kjj
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-D9L / Putative beta-lactamase
Similarity search - Component
Biological speciesJeotgalibacillus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.492 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 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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)44,4432
Polymers44,2231
Non-polymers2191
Water1,44180
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)117.988, 117.988, 52.370
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-501-

HOH

21A-520-

HOH

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Components

#1: Protein Putative beta-lactamase / MlnI


Mass: 44223.426 Da / Num. of mol.: 1 / Mutation: S73A
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-D9L / 4-(2-acetamidoethylsulfanyl)-4-oxidanylidene-butanoic acid


Mass: 219.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.3, 25 % PEG3350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.49→117.99 Å / Num. obs: 13437 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.028 / Rrim(I) all: 0.102 / Net I/σ(I): 22.5 / Num. measured all: 184221
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
2.49-2.5614.50.343136909460.9820.0930.3569.1100
11.15-117.999.60.05418261900.9980.0170.05732.297.1

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KJH

6kjh


Resolution: 2.492→39.165 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.34
RfactorNum. reflection% reflection
Rfree0.2527 1340 10 %
Rwork0.2029 --
obs0.2078 13397 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.2 Å2 / Biso mean: 37.4035 Å2 / Biso min: 10.52 Å2
Refinement stepCycle: final / Resolution: 2.492→39.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 0 14 80 2938
Biso mean--74.1 32.72 -
Num. residues----361
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4922-2.58130.29641300.23921176100
2.5813-2.68460.2841310.22481168100
2.6846-2.80680.32371320.2271187100
2.8068-2.95470.27081310.22651185100
2.9547-3.13970.28321320.21851187100
3.1397-3.3820.25341330.21991194100
3.382-3.72210.30221340.24061213100
3.7221-4.26020.20941340.1782120199
4.2602-5.36520.19211370.15921238100
5.3652-39.1650.23941460.1845130899
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)
13.27790.6734-0.52314.7744-1.78362.52390.0754-0.05470.3095-0.0256-0.1456-0.4061-0.11280.34050.04210.17130.0064-0.02750.2066-0.04370.322140.4549-28.707272.3221
22.08230.45540.44361.55610.13862.0741-0.23120.40540.4056-0.36410.13470.2076-0.23240.01730.03330.2685-0.028-0.05910.18270.05720.299112.981-26.079352.8712
32.68080.56970.71713.1131-0.54791.7354-0.15170.11510.2753-0.03180.04640.0222-0.27020.28680.07340.2459-0.032-0.01480.1854-0.01910.2406121.7456-18.474566.4949
43.7666-0.172-1.46174.26250.42346.4328-0.05650.2701-0.1778-0.28380.0552-0.23630.26080.01480.03160.12910.0071-0.05460.13620.01950.2234117.5693-38.650562.0605
54.7881-0.8552.43235.34561.75952.2528-0.0450.37310.0405-0.34620.1072-0.26820.01080.07960.00210.1587-0.01420.0270.23870.00350.2732132.2499-37.720766.082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 61 )A6 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 180 )A62 - 180
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 255 )A181 - 255
4X-RAY DIFFRACTION4chain 'A' and (resid 256 through 302 )A256 - 302
5X-RAY DIFFRACTION5chain 'A' and (resid 303 through 366 )A303 - 366

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