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

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Basic information

Entry
Database: PDB / ID: 6kjt
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 / homologyBeta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / SUCCINIC ACID / Putative beta-lactamase
Function and homology information
Biological speciesJeotgalibacillus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 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
B: Putative beta-lactamase
C: Putative beta-lactamase
D: Putative beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,4308
Polymers176,9584
Non-polymers4724
Water15,025834
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)128.431, 132.422, 110.820
Angle α, β, γ (deg.)90.000, 117.340, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative beta-lactamase / BmmI


Mass: 44239.426 Da / Num. of mol.: 4
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-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 834 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 10 % Tacsimate, pH 6.0, and 26 % PEG3350

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.11→57.043 Å / Num. obs: 88701 / % possible obs: 94.3 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.06 / Rrim(I) all: 0.113 / Net I/σ(I): 7.4
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
2.11-2.233.40.46644144131470.8580.2990.5562.595.8
6.68-57.043.50.0471055930060.9940.0290.0561598.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KJH

6kjh


Resolution: 2.113→57.04 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.09
RfactorNum. reflection% reflection
Rfree0.2153 4399 4.96 %
Rwork0.1622 --
obs0.1648 88683 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.25 Å2 / Biso mean: 40.2478 Å2 / Biso min: 15.23 Å2
Refinement stepCycle: final / Resolution: 2.113→57.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11255 0 0 834 12089
Biso mean---42.29 -
Num. residues----1433
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.113-2.13650.32671550.267272891
2.1365-2.16160.33811420.2543271193
2.1616-2.1880.29311530.2387293199
2.188-2.21570.27061650.2327298099
2.2157-2.24490.3761770.232170394
2.2449-2.27560.2708410.259974688
2.2756-2.30810.25851390.2122298799
2.3081-2.34260.25711630.18542923100
2.3426-2.37920.25981370.1813295799
2.3792-2.41820.2541640.18922933100
2.4182-2.45990.24651570.17522996100
2.4599-2.50460.23491610.17352950100
2.5046-2.55280.22381440.176294199
2.5528-2.60490.24941550.1858295399
2.6049-2.66150.26151390.1816295299
2.6615-2.72350.22681630.1759293498
2.7235-2.79160.24761480.1723294198
2.7916-2.8670.2511420.1755291098
2.867-2.95140.22391490.1772287597
2.9514-3.04670.24041400.1843278293
3.0467-3.15550.23011420.181284194
3.1555-3.28190.21551630.1762964100
3.2819-3.43120.22091600.16582983100
3.4312-3.61210.22011550.15612952100
3.6121-3.83840.18591570.1307299699
3.8384-4.13460.20151630.1254294099
4.1346-4.55060.14031560.1127295999
4.5506-5.20870.15891580.1223293898
5.2087-6.56080.18831500.1519288096
6.5608-57.040.18821610.149299898
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)
13.7246-0.16160.84972.2126-0.03691.0070.23710.0753-0.424-0.147-0.08820.20530.2471-0.1491-0.13330.2934-0.0733-0.04250.25450.0480.2312-19.105713.555926.7802
22.2826-0.1833-0.54171.1334-0.39632.9184-0.01270.088-0.126-0.1009-0.022-0.07510.06790.29170.0410.19730.01820.00980.18710.010.236413.249124.572525.3104
31.3993-0.0574-0.06032.0782-0.11481.4890.02480.0488-0.1425-0.1153-0.0309-0.01340.156-0.02720.02140.20860.0008-0.02480.20620.00510.1854-1.538619.601931.851
43.11770.68450.76134.5469-1.29970.70490.04970.2669-0.1212-0.4418-0.0291-0.15940.14620.0568-0.02040.26260.0155-0.02890.257-0.00930.1755-14.612426.177223.9857
50.8159-0.44380.14492.51220.30521.05250.03370.0703-0.1214-0.2382-0.02550.42140.093-0.1414-0.01940.3027-0.0018-0.06620.27310.04030.2714-3.2396-18.722547.5231
61.39540.01640.4511.92650.12852.6887-0.0411-0.31250.19080.1816-0.00030.4159-0.2177-0.4850.09260.29830.0470.01350.3385-0.0120.3473-7.0493.13963.787
72.80720.6311-0.2224.3248-1.28874.2779-0.070.01050.1698-0.383-0.04470.7609-0.1222-0.71090.01980.36390.0009-0.10240.48310.01740.4845-18.3143-10.203645.2876
81.9088-0.06451.02422.91360.30682.14320.0837-0.0989-0.057-0.058-0.03970.0796-0.0668-0.10650.07020.265-0.0122-0.0280.17140.0340.1923.0151-4.631154.2149
91.52190.4184-0.54093.2932-0.54562.4912-0.0965-0.5095-0.60090.52850.02030.58370.3462-0.53940.02390.3997-0.03810.07840.40870.04880.4163-0.5841-12.491970.0647
101.7259-0.4171.25313.1916-0.04762.24560.0113-0.1858-0.04920.17420.06310.26280.075-0.2635-0.14320.2729-0.0019-0.02340.21560.0270.24612.9752-20.595356.7817
110.7552-0.1958-0.41561.62490.63141.14250.04440.10850.0608-0.1552-0.13640.2661-0.099-0.30470.05850.1670.0345-0.04540.3349-0.02270.235730.278-23.33275.8112
120.8401-0.80360.55530.8669-0.47450.34080.31180.2393-0.1052-0.5598-0.42970.5647-0.2155-0.35030.12530.44460.0903-0.11810.6335-0.09670.523118.0783-22.6445-2.4858
130.9593-0.336-0.17833.19080.58450.9394-0.0135-0.00390.1516-0.061-0.05190.1234-0.1581-0.19830.07230.19760.069-0.02830.3112-0.01550.239633.6721-15.868815.1216
141.631-0.09760.85761.3627-0.02441.9391-0.08150.26140.29530.0140.0012-0.0344-0.31040.09240.07030.29240.06-0.00110.25050.04210.290948.539317.169518.9861
152.48451.20370.2493.313-0.10442.4557-0.06780.16020.36840.14090.04220.0008-0.3754-0.0760.00590.26010.1071-0.03440.24310.00260.285745.276617.311824.1735
166.21051.6878-1.86814.1947-1.02296.1386-0.11290.2567-0.2435-0.0455-0.3784-0.859-0.21961.15370.44370.30370.0808-0.00360.57320.08010.373958.92725.756716.4284
173.18870.05410.80214.20821.6861.9788-0.09720.2280.0901-0.00920.0801-0.1151-0.30380.14430.02830.31660.028-0.05760.23-0.01320.218957.988910.354231.6277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 74 )A7 - 74
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 180 )A75 - 180
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 301 )A181 - 301
4X-RAY DIFFRACTION4chain 'A' and (resid 302 through 364 )A302 - 364
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 88 )B7 - 88
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 206 )B89 - 206
7X-RAY DIFFRACTION7chain 'B' and (resid 207 through 225 )B207 - 225
8X-RAY DIFFRACTION8chain 'B' and (resid 226 through 283 )B226 - 283
9X-RAY DIFFRACTION9chain 'B' and (resid 284 through 302 )B284 - 302
10X-RAY DIFFRACTION10chain 'B' and (resid 303 through 364 )B303 - 364
11X-RAY DIFFRACTION11chain 'C' and (resid 7 through 206 )C7 - 206
12X-RAY DIFFRACTION12chain 'C' and (resid 207 through 235 )C207 - 235
13X-RAY DIFFRACTION13chain 'C' and (resid 236 through 365 )C236 - 365
14X-RAY DIFFRACTION14chain 'D' and (resid 7 through 206 )D7 - 206
15X-RAY DIFFRACTION15chain 'D' and (resid 207 through 283 )D207 - 283
16X-RAY DIFFRACTION16chain 'D' and (resid 284 through 302 )D284 - 302
17X-RAY DIFFRACTION17chain 'D' and (resid 303 through 364 )D303 - 364

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