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- PDB-6xfr: Metallo-beta-lactamase from Pontibacter korlensis -

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Basic information

Entry
Database: PDB / ID: 6xfr
TitleMetallo-beta-lactamase from Pontibacter korlensis
ComponentsLactamase_B domain-containing protein
KeywordsHYDROLASE / B1 Metallo-beta-lactamase / metallohydrolase / metalloenzyme
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
B2 metallo-beta-lactamase
Similarity search - Component
Biological speciesPontibacter korlensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.608 Å
AuthorsSchenk, G. / Schembri, M.A. / Prombhul, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: Metallo-beta-lactamase from Pontibacter korlensis
Authors: Schenk, G. / Schembri, M.A. / Prombhul, S.
History
DepositionJun 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Lactamase_B domain-containing protein
B: Lactamase_B domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,65225
Polymers49,5102
Non-polymers2,14223
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-543 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.941, 97.941, 103.237
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 218 or resid 219 through 301))
21(chain B and (resid 7 through 218 or resid 219 through 301))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 7 through 218 or resid 219 through 301))A7 - 218
121(chain A and (resid 7 through 218 or resid 219 through 301))A219 - 301
211(chain B and (resid 7 through 218 or resid 219 through 301))B7 - 218
221(chain B and (resid 7 through 218 or resid 219 through 301))B219 - 301

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lactamase_B domain-containing protein


Mass: 24755.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pontibacter korlensis (bacteria) / Gene: PKOR_06505 / Plasmid: pET-30a(+) / Cell (production host): Bacteria / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 (DE3) pLysS / References: UniProt: A0A0E3ZJD7

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Non-polymers , 5 types, 43 molecules

#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris, 0.002 M ZnCl2, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.6→48.97 Å / Num. obs: 15978 / % possible obs: 99.8 % / Redundancy: 1 % / CC1/2: 0.997 / Net I/σ(I): 0.08
Reflection shellResolution: 2.6→2.6 Å / Num. unique obs: 15976 / CC1/2: 0.997

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c09

4c09


Resolution: 2.608→44.245 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 771 4.96 %
Rwork0.1763 14779 -
obs0.1792 15550 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 263.95 Å2 / Biso mean: 42.9972 Å2 / Biso min: 0.48 Å2
Refinement stepCycle: final / Resolution: 2.608→44.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 199 20 3488
Biso mean--78.94 29.04 -
Num. residues----425
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1306X-RAY DIFFRACTION9.014TORSIONAL
12B1306X-RAY DIFFRACTION9.014TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7713-2.77130.33641380.2379237397
2.9852-2.98520.3151470.2369238698
3.2855-3.28550.30491100.1997245399
3.7607-3.76070.21321300.1746247999
4.7373-4.73730.19131340.1453247698
4.7374-4.73740.20641120.1573261297
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)
13.8701-3.9071.63254.3303-0.5273.331-0.18620.12680.09570.08580.05090.0222-0.4798-0.11840.10680.3770.0163-0.00550.22250.02090.206844.131825.708313.1143
23.69191.73193.54438.0967-0.93454.3226-0.2586-0.03530.7565-0.1849-0.21790.1085-1.0428-0.05260.63790.51370.03140.05610.2322-0.02640.316649.625334.607110.1314
37.81611.52412.17010.9538-0.2314.76880.01290.50660.3819-0.1421-0.01120.1557-0.4138-0.1369-0.00110.35630.08760.03990.23060.0190.233646.204923.7654-1.428
45.02560.5993-0.7612.01040.59813.6354-0.06910.1592-0.1504-0.13570.08620.08040.1975-0.3558-0.00660.27310.0089-0.03180.20220.01690.184838.490711.804810.2964
59.3781-5.8622.97525.796-1.92250.9457-0.4117-0.54430.52850.1760.7743-0.7661-0.8584-0.1838-0.45341.26630.2853-0.2281.1979-0.49730.701221.95994.344811.4424
68.60225.1520.66166.40281.40347.2454-0.056-0.10560.62070.10680.00780.3485-0.8724-0.03440.04030.33030.1055-0.00910.30610.00560.204534.173521.896933.6039
78.34023.78724.70254.69090.41433.6350.36420.49680.56260.0118-0.06170.7171-0.8212-0.9031-0.0960.42480.19650.07870.55560.04870.381124.343224.051136.3619
84.81411.446-0.49131.96660.61696.17060.0828-0.50330.35390.3577-0.17550.0558-0.42360.19620.08120.3492-0.0013-0.0030.28090.0240.231736.81916.737146.6631
95.2365-0.76420.44591.4029-2.08124.92260.0681-0.39890.44270.3532-0.0003-0.1141-0.49970.1535-0.08340.30550.0163-0.01450.3212-0.04280.229347.440119.531635.605
106.74233.65491.1627.76840.03995.2099-0.00460.0075-0.0688-0.2183-0.0479-0.56050.10820.8127-0.01770.2111-0.01050.03810.37140.00050.190852.14716.404733.991
112.02112.4929-2.63923.708-3.65123.6938-0.2279-0.39610.40310.6208-0.1411-1.0984-1.076-0.14690.25111.09130.2186-0.31660.95720.16380.693663.894122.164334.7416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 52 )A9 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 66 )A53 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 122 )A67 - 122
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 218 )A123 - 218
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 219 )A219
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 52 )B9 - 52
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 66 )B53 - 66
8X-RAY DIFFRACTION8chain 'B' and (resid 67 through 146 )B67 - 146
9X-RAY DIFFRACTION9chain 'B' and (resid 147 through 177 )B147 - 177
10X-RAY DIFFRACTION10chain 'B' and (resid 178 through 218 )B178 - 218
11X-RAY DIFFRACTION11chain 'B' and (resid 219 through 219 )B219

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