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

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Basic information

Entry
Database: PDB / ID: 6kjp
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 / Chem-D9F / Putative beta-lactamase
Function and homology information
Biological speciesJeotgalibacillus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 1.1Dec 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)44,7383
Polymers44,2391
Non-polymers4992
Water3,603200
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 area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.640, 119.640, 51.780
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-569-

HOH

21A-617-

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: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
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 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.06→84.6 Å / Num. obs: 20392 / % possible obs: 86.1 % / Redundancy: 6.3 % / CC1/2: 0.978 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.078 / Rrim(I) all: 0.209 / Net I/σ(I): 7.2 / Num. measured all: 128937 / Scaling rejects: 245
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
2.06-2.125.11.55715813910.2870.7111.7141.278
8.98-84.6110.09939053540.9910.0310.10418.299.2

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Processing

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

6kjh


Resolution: 2.06→51.78 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 1996 9.82 %
Rwork0.2027 18327 -
obs0.2083 20323 85.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.71 Å2 / Biso mean: 29.9392 Å2 / Biso min: 11.43 Å2
Refinement stepCycle: final / Resolution: 2.06→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 34 200 3057
Biso mean--65.31 34.25 -
Num. residues----358
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0601-2.11160.33051240.2798113775
2.1116-2.16870.32311240.2743114376
2.1687-2.23250.32491250.28114376
2.2325-2.30460.31031260.2631115277
2.3046-2.3870.32791290.2522118878
2.387-2.48250.37821350.3144122681
2.4825-2.59550.30571370.2422127583
2.5955-2.73240.26011370.2247125783
2.7324-2.90350.27571410.2158128485
2.9035-3.12770.28331450.2088133487
3.1277-3.44240.25471540.1944141691
3.4424-3.94040.21151650.1516151898
3.9404-4.96380.18941720.14871580100
4.9638-51.780.23791820.1758167499
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)
13.02061.4184-0.30494.3659-1.70172.7672-0.047-0.23480.16030.3735-0.0116-0.6093-0.12360.421-0.00440.1333-0.0029-0.05090.2664-0.030.253825.82383.3418124.2624
21.31140.0815-0.07951.3356-0.0171.0904-0.13220.20950.2746-0.21390.08480.0178-0.1820.0201-0.01220.1787-0.05120.00030.11650.02860.17933.975492.4328111.4078
31.7804-0.33990.10322.6891-0.57661.3639-0.1630.64260.2986-0.56110.09320.3321-0.2308-0.0144-0.0510.3457-0.1082-0.08720.26510.07940.2526-3.675595.085896.0775
41.28180.33630.23131.3382-0.13460.9332-0.12540.14920.3497-0.02720.08980.1556-0.39150.21010.00080.2461-0.0686-0.02130.15670.02180.24511.8195101.9335114.1569
51.9020.35590.12471.5977-0.27191.2874-0.0204-0.1371-0.0382-0.00670.0819-0.0413-0.0869-0.0916-0.03890.1218-0.0381-0.00530.0939-0.05050.1437-0.052484.9335120.8981
61.4175-0.21850.72280.534-0.00860.8311-0.12610.3191-0.1154-0.32690.0013-0.16450.02110.1444-0.03850.2032-0.0220.02380.2263-0.03610.24018.823578.7321108.185
72.30520.212-0.16242.2792-0.31861.67410.07330.14080.0089-0.0604-0.0055-0.19360.0220.11320.00480.11580.0055-0.01360.1177-0.04270.220116.517782.8252117.7622
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 134 )A28 - 134
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 165 )A135 - 165
4X-RAY DIFFRACTION4chain 'A' and (resid 166 through 235 )A166 - 235
5X-RAY DIFFRACTION5chain 'A' and (resid 236 through 283 )A236 - 283
6X-RAY DIFFRACTION6chain 'A' and (resid 284 through 323 )A284 - 323
7X-RAY DIFFRACTION7chain 'A' and (resid 324 through 364 )A324 - 364

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