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

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Basic information

Entry
Database: PDB / ID: 6kjh
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: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta / Putative beta-lactamase
Function and homology information
Biological speciesJeotgalibacillus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsXiao, F. / Sheng, D. / 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 1.1Sep 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)44,3352
Polymers44,2391
Non-polymers961
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-20 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.476, 118.476, 51.874
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-675-

HOH

21A-744-

HOH

31A-776-

HOH

41A-858-

HOH

51A-873-

HOH

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Components

#1: Protein Putative beta-lactamase / MlnI


Mass: 44239.426 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 40.21 %
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: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.68→118.48 Å / Num. obs: 42566 / % possible obs: 99.8 % / Redundancy: 13.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.044 / Rrim(I) all: 0.163 / Net I/σ(I): 13.1 / Num. measured all: 568360
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
1.68-1.729.61.0182900530210.7590.3431.0752.297.5
7.51-118.4810.80.05661895720.9980.0170.05831.799.7

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IVI

4ivi


Resolution: 1.68→59.238 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.48
RfactorNum. reflection% reflection
Rfree0.1892 2000 4.71 %
Rwork0.1644 --
obs0.1656 42481 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 181.19 Å2 / Biso mean: 28.0233 Å2 / Biso min: 9.24 Å2
Refinement stepCycle: final / Resolution: 1.68→59.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 5 389 3247
Biso mean--18.29 32.8 -
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 (%)
1.68-1.72210.25671370.2196277197
1.7221-1.76860.21341390.1916283899
1.7686-1.82070.19721410.17792838100
1.8207-1.87940.24141420.18332867100
1.8794-1.94660.2781410.24072856100
1.9466-2.02460.19561410.16052865100
2.0246-2.11670.17891420.15392876100
2.1167-2.22830.18181420.15192871100
2.2283-2.36790.17821430.17482877100
2.3679-2.55080.19151420.15082889100
2.5508-2.80740.20261440.15452909100
2.8074-3.21370.16241450.1612940100
3.2137-4.04870.16741470.14272955100
4.0487-59.2380.18251540.16583129100
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)
13.3647-0.71441.33531.6389-0.38821.8461-0.1211-0.10240.26220.03440.02040.025-0.1532-0.06820.09660.14740.010.0110.1237-0.03470.125428.817522.568371.1844
20.7798-0.1916-0.15591.06980.27770.84140.03410.1221-0.108-0.1408-0.03130.01760.0481-0.04060.0010.12130.0101-0.00720.1449-0.01920.133428.4053-4.887855.9949
37.58530.5466-1.48274.65571.81775.14590.06650.6125-0.0344-0.4613-0.14850.2538-0.1196-0.798-0.06750.21550.0347-0.0530.3229-0.03380.195915.7532-4.762243.7881
40.9236-0.37890.03111.11930.25470.93770.0490.0599-0.0123-0.0874-0.06190.1064-0.0266-0.14730.01670.11930.0015-0.01490.1555-0.00670.14419.9960.943459.3426
51.9489-1.02210.4231.9594-0.02441.08470.0134-0.0705-0.01070.10150.012-0.09760.06560.0245-0.01620.0984-0.00770.00450.0830.00180.094934.3331-0.566769.2452
61.46470.4273-0.54714.3348-3.36112.9268-0.07150.23410.4312-0.1421-0.0333-0.403-0.20480.13260.170.1972-0.02350.02320.18620.05490.257538.98465.614251.1636
72.4566-0.30810.09291.88450.04140.80740.00740.08240.0507-0.0216-0.0072-0.0639-0.03750.0160.00860.1164-0.00670.0010.1121-0.00640.110938.001414.330964.9376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 61 )A7 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 130 )A62 - 130
3X-RAY DIFFRACTION3chain 'A' and (resid 131 through 151 )A131 - 151
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 235 )A152 - 235
5X-RAY DIFFRACTION5chain 'A' and (resid 236 through 283 )A236 - 283
6X-RAY DIFFRACTION6chain 'A' and (resid 284 through 302 )A284 - 302
7X-RAY DIFFRACTION7chain 'A' and (resid 303 through 365 )A303 - 365

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