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- PDB-7q0y: Crystal structure of CTX-M-14 in complex with Bortezomib -

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Basic information

Entry
Database: PDB / ID: 7q0y
TitleCrystal structure of CTX-M-14 in complex with Bortezomib
ComponentsBeta-lactamase
KeywordsHYDROLASE / Lactamase / Antibiotic / Resistence
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-BO2 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWerner, N. / Perbandt, M. / Hinrichs, W. / Prester, A. / Rohde, H. / Aepfelbacher, M. / Betzel, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Sci Rep / Year: 2022
Title: Structural basis to repurpose boron-based proteasome inhibitors Bortezomib and Ixazomib as beta-lactamase inhibitors.
Authors: Perbandt, M. / Werner, N. / Prester, A. / Rohde, H. / Aepfelbacher, M. / Hinrichs, W. / Betzel, C.
History
DepositionOct 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5725
Polymers28,0021
Non-polymers5714
Water8,377465
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-15 kcal/mol
Surface area10710 Å2
Unit cell
Length a, b, c (Å)41.303, 62.331, 86.244
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 28001.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S1JJX2, beta-lactamase

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Non-polymers , 5 types, 469 molecules

#2: Chemical ChemComp-BO2 / N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / BORTEZOMIB


Mass: 384.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25BN4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticancer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30 % PEG8000, 0.2 M lithium sulfate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.3→35.46 Å / Num. obs: 55064 / % possible obs: 99 % / Redundancy: 7.1 % / Biso Wilson estimate: 9.85 Å2 / CC1/2: 1 / Rrim(I) all: 0.073 / Net I/σ(I): 16.89
Reflection shellResolution: 1.3→1.35 Å / Mean I/σ(I) obs: 3.59 / Num. unique obs: 38038 / CC1/2: 0.971 / Rrim(I) all: 0.527 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GTH

6gth


Resolution: 1.3→43.12 Å / SU ML: 0.0889 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.8874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1439 3791 3.62 %
Rwork0.1278 100865 -
obs0.1284 104656 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.2 Å2
Refinement stepCycle: LAST / Resolution: 1.3→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 39 465 2465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01022068
X-RAY DIFFRACTIONf_angle_d1.22382823
X-RAY DIFFRACTIONf_chiral_restr0.086334
X-RAY DIFFRACTIONf_plane_restr0.0133372
X-RAY DIFFRACTIONf_dihedral_angle_d13.8236768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.23291310.22213404X-RAY DIFFRACTION90.11
1.31-1.330.20171340.20183630X-RAY DIFFRACTION95.03
1.33-1.350.18511360.19453633X-RAY DIFFRACTION96.96
1.35-1.370.23191380.19923644X-RAY DIFFRACTION95.99
1.37-1.390.18741350.18263733X-RAY DIFFRACTION97.48
1.39-1.410.18211420.18283700X-RAY DIFFRACTION98.24
1.41-1.430.1851390.16763713X-RAY DIFFRACTION97.79
1.43-1.460.1751410.16113775X-RAY DIFFRACTION99.37
1.46-1.490.1851410.1523717X-RAY DIFFRACTION98.32
1.49-1.510.16871430.14843802X-RAY DIFFRACTION99.5
1.51-1.550.17971400.14463738X-RAY DIFFRACTION98.88
1.55-1.580.18091350.14033758X-RAY DIFFRACTION99.34
1.58-1.620.14921410.13463758X-RAY DIFFRACTION99.19
1.62-1.660.16981440.13473792X-RAY DIFFRACTION99.14
1.66-1.70.15431420.13193761X-RAY DIFFRACTION99.74
1.7-1.750.13171380.12343789X-RAY DIFFRACTION99.47
1.75-1.810.14821450.12223782X-RAY DIFFRACTION99.62
1.81-1.870.13841410.12413836X-RAY DIFFRACTION99.62
1.87-1.950.14731400.11533697X-RAY DIFFRACTION99.43
1.95-2.040.11471460.11123793X-RAY DIFFRACTION99.34
2.04-2.140.13051410.10633771X-RAY DIFFRACTION99.57
2.14-2.280.13071420.10453803X-RAY DIFFRACTION99.57
2.28-2.450.11091460.10993758X-RAY DIFFRACTION99.72
2.45-2.70.11311410.1153778X-RAY DIFFRACTION99.54
2.7-3.090.11561410.11233763X-RAY DIFFRACTION98.94
3.09-3.890.13161470.11023762X-RAY DIFFRACTION99.62
3.89-43.120.15161410.12883775X-RAY DIFFRACTION99.21
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)
12.242631997541.0678269041-0.1123920247662.384693648920.9471627297672.44277666126-0.05887054368320.184078313518-0.0971515031343-0.1269235733260.103408838669-0.05126017684040.05809480269860.0806345683458-0.04060379387180.06587954325790.00585748388033-0.005935159942070.0516384481753-0.005109529743330.050023978370310.3171912437-15.5004951166-22.9188347372
20.982560643037-0.41688674931-0.4060541385190.7365133163560.4798571487760.811863490091-0.0355574140764-0.00567605002975-0.1110348835320.0498281481725-0.01945570002720.06601252810950.0920477665441-0.0202499510550.05400630581980.0798092471365-0.004961743984610.003560777498270.07162273017850.005343919015530.06435193744482.61522473551-9.48363007832-7.57269694484
36.775036166394.04237973956-2.077384062764.48942275891-0.1568511242891.854051713970.243496075938-0.5712033460260.39848944410.292983894758-0.2998855074890.3584366729680.02038468620920.07484838158180.04083469104040.100982371535-0.005589703586880.0101308754740.111262240271-0.01921070271920.0662675430427-3.8884307101610.358261696.19459880402
42.561418998990.163857727503-0.9971422678791.027783819780.0962615554031.000162111310.087562966817-0.07576302066830.2654597523820.0391363041031-0.01194372260420.0225301777299-0.121088507920.0378322586745-0.06705345643240.077440401396-0.0007544841192880.0006709845643930.0703323132087-0.008582577711060.07326596958211.1434130236613.2695606968-3.2232998709
50.706980260374-0.218218718148-0.1479301625170.5423328626010.02173197537770.291438998712-0.0190017313104-0.125398802207-0.03498393403080.06122434821080.0231524890398-0.007163099525470.007414595207170.046581393722-0.006024834205090.091884345818-0.0015789568098-0.008402067267090.1052166345160.003061782983490.07176731316388.47697187935-2.06672819682-0.280932673953
68.33951764178-3.024756240191.198380148971.33347206392-0.05166751476181.1569965576-0.003048112851660.00353182948258-0.233612344623-0.0423982135537-0.00715277323680.1239961945280.0679331957802-0.04006253732320.02277874447370.0700757222151-0.007963868132860.004857347481490.05712307800210.01045852003590.04471413594071.07623305626-12.2917578623-7.74829888613
71.000254865980.103664034926-0.1201356716120.526444144298-0.001590960740760.3237781111840.002936365924870.12990562775-0.0195612914958-0.07540235732650.03645521218430.04145522664030.0477290040645-0.104149019201-0.02424799093660.068597379265-0.00609401151944-0.0129388903540.07984534171170.0004151113828240.0488970234149-6.55018719969-2.31259515025-13.3872717754
84.360376066380.1625314254720.4340398787030.803368303961-0.1574797027650.948235491174-0.02811469911680.0921133588739-0.0436020843212-0.04722265305050.02172169785490.00223622898408-0.00508306621178-0.008531587072290.01844212050590.06128123367930.00343609879597-0.003751930384950.0514433487583-0.01168929821840.02753600907276.16314008705-4.43055320684-16.9101016371
97.624503991425.927145027142.242793925867.456429951882.365690779975.99690832888-0.1496151367510.199425653024-0.0310436861629-0.2362976671970.02952046709470.1845419448360.102252593861-0.160953421380.08421650874260.07856879466740.00501105810773-0.002808589931970.0873279022826-0.01449146042340.06367414839054.0699808649-8.33679255305-25.636300796
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 50 )25 - 501 - 26
22chain 'A' and (resid 51 through 85 )51 - 8527 - 60
33chain 'A' and (resid 86 through 101 )86 - 10161 - 76
44chain 'A' and (resid 102 through 128 )102 - 12877 - 103
55chain 'A' and (resid 129 through 179 )129 - 179104 - 154
66chain 'A' and (resid 180 through 194 )180 - 194155 - 169
77chain 'A' and (resid 195 through 229 )195 - 229170 - 204
88chain 'A' and (resid 230 through 274 )230 - 274205 - 248
99chain 'A' and (resid 275 through 289 )275 - 289249 - 263

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