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- PDB-5odz: CRYSTAL STRUCTURE OF THE BETA-LACTAMASE OXA-163 -

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Basic information

Entry
Database: PDB / ID: 5odz
TitleCRYSTAL STRUCTURE OF THE BETA-LACTAMASE OXA-163
ComponentsBeta-lactamase
KeywordsANTIBIOTIC / antibiotic resistance / oxacillinase / OXA-48-like / cephalosporinase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsLund, B.A. / Carlsen, T.J.O. / Leiros, H.K.S.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structure, activity and thermostability investigations of OXA-163, OXA-181 and OXA-245 using biochemical analysis, crystal structures and differential scanning calorimetry analysis.
Authors: Lund, B.A. / Thomassen, A.M. / Carlsen, T.J.O. / Leiros, H.K.S.
History
DepositionJul 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,24310
Polymers58,8782
Non-polymers3658
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, The homolog OXA-48 has been shown to be a dimer in solution by SEC. Our DSC results with OXA-163 and OXA-48 indicate that OXA-163 is also a dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-56 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.920, 121.920, 160.426
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-401-

HOH

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Components

#1: Protein Beta-lactamase / OXA-163


Mass: 29439.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal His-Tag cleaved off with TEV protease / Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: blaOXA-163 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR pRARE / References: UniProt: F6KZJ2, beta-lactamase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M Tris pH 9.0 28 % PEG500 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.07→24.49 Å / Num. obs: 43401 / % possible obs: 99.9 % / Redundancy: 11 % / Rmerge(I) obs: 0.1538 / Rrim(I) all: 0.1614 / Net I/σ(I): 12.66
Reflection shellResolution: 2.07→2.144 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.8563 / Num. unique obs: 4244 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimless0.5.31data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2L

4s2l


Resolution: 2.07→24.486 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1867 2186 5.04 %
Rwork0.1452 --
obs0.1473 43401 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→24.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 17 368 4254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114089
X-RAY DIFFRACTIONf_angle_d1.195537
X-RAY DIFFRACTIONf_dihedral_angle_d15.1251506
X-RAY DIFFRACTIONf_chiral_restr0.054575
X-RAY DIFFRACTIONf_plane_restr0.006715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.1150.23971260.18752512X-RAY DIFFRACTION100
2.115-2.16420.19761460.1772499X-RAY DIFFRACTION100
2.1642-2.21830.20011270.15512549X-RAY DIFFRACTION100
2.2183-2.27820.21381490.16292504X-RAY DIFFRACTION100
2.2782-2.34520.19761240.15082572X-RAY DIFFRACTION100
2.3452-2.42080.17371450.14132504X-RAY DIFFRACTION100
2.4208-2.50730.20671390.13382549X-RAY DIFFRACTION100
2.5073-2.60750.16821310.13392564X-RAY DIFFRACTION100
2.6075-2.72610.1871340.13182548X-RAY DIFFRACTION100
2.7261-2.86960.19021410.13332552X-RAY DIFFRACTION100
2.8696-3.04910.20831390.13812589X-RAY DIFFRACTION100
3.0491-3.2840.19141240.14052577X-RAY DIFFRACTION100
3.284-3.61350.15211310.13142597X-RAY DIFFRACTION100
3.6135-4.13420.14031460.1222622X-RAY DIFFRACTION100
4.1342-5.20050.18291240.1342674X-RAY DIFFRACTION100
5.2005-24.48760.2291600.19452803X-RAY DIFFRACTION100
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)
16.65590.08553.23837.1981-0.29019.33750.04510.1765-1.06350.38770.0452-0.70841.34260.2839-0.10470.60410.0130.15650.24450.03290.7365-50.5113-7.2475-22.418
25.0562-0.40121.12997.948-4.85692.0854-0.31380.162-0.4088-0.22780.2405-0.23910.524-0.10950.08930.3836-0.05690.10140.1536-0.0470.3069-53.4146-1.5821-26.314
31.9164-0.5228-0.36986.05851.0431.6825-0.0948-0.0125-0.22530.09690.03620.11110.3676-0.07670.04460.1889-0.04090.02150.14750.00520.1226-61.455310.4488-17.1706
45.9754-0.07663.61312.45690.36529.747-0.2294-0.29760.19830.34060.0591-0.0921-0.7270.13670.18960.221-0.0105-0.00680.1211-0.0360.1956-55.140828.5914-8.9646
54.09280.76170.27741.82650.36592.3163-0.0498-0.14770.03810.1244-0.00910.0033-0.107-0.06360.07980.1970.0079-0.00260.12390.02260.1191-61.939720.3133-12.5163
62.33731.6669-2.49594.0524-2.46313.6907-0.1410.2304-0.0403-0.13910.17080.08950.2463-0.3102-0.0440.1279-0.046-0.02580.158-0.00380.1238-60.935814.8168-23.5903
74.25251.424-0.93964.6599-0.71263.4906-0.1892-0.2143-0.35190.1289-0.0117-0.19540.36180.17380.21280.17510.00920.01610.10740.02690.188-49.61218.2825-20.6233
85.0046-0.706-3.74216.4614.68859.1334-0.3857-0.12-0.21770.5082-0.0363-0.50890.90620.82710.48130.38160.08730.0410.28170.1250.464-43.68141.9995-19.0112
93.8911-1.3335-2.2346.52332.17147.405-0.1542-0.77060.03180.48370.5643-0.9528-0.35691.6554-0.33260.343-0.1861-0.13270.64560.02010.6347-21.497336.2227-21.7338
101.14310.06410.29751.30270.12042.42880.04650.01130.04510.0495-0.0561-0.1683-0.13270.19030.00750.1352-0.05340.00320.15760.01420.1891-38.292729.764-40.5709
112.13180.6137-0.38061.696-1.08893.30570.0742-0.1676-0.05170.1057-0.1317-0.2442-0.19560.32370.05630.1522-0.0573-0.02070.1581-0.00220.1745-37.355531.2388-31.3646
123.5813-0.7274-3.32653.48493.92382.0381-0.1976-0.6134-0.56770.40620.0868-0.1660.61321.14260.12920.3749-0.0031-0.08590.69250.28410.6513-25.768425.0887-23.8479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 23 through 38 )
2X-RAY DIFFRACTION2chain 'B' and (resid 39 through 58 )
3X-RAY DIFFRACTION3chain 'B' and (resid 59 through 82 )
4X-RAY DIFFRACTION4chain 'B' and (resid 83 through 102 )
5X-RAY DIFFRACTION5chain 'B' and (resid 103 through 155 )
6X-RAY DIFFRACTION6chain 'B' and (resid 156 through 194 )
7X-RAY DIFFRACTION7chain 'B' and (resid 195 through 243 )
8X-RAY DIFFRACTION8chain 'B' and (resid 244 through 265 )
9X-RAY DIFFRACTION9chain 'D' and (resid 23 through 38 )
10X-RAY DIFFRACTION10chain 'D' and (resid 39 through 155 )
11X-RAY DIFFRACTION11chain 'D' and (resid 156 through 243 )
12X-RAY DIFFRACTION12chain 'D' and (resid 244 through 265 )

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