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- PDB-3e2l: Crystal Structure of the KPC-2 Beta-lactamase/Beta-lactamase inhi... -

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Basic information

Entry
Database: PDB / ID: 3e2l
TitleCrystal Structure of the KPC-2 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP)
Components
  • Beta-lactamase inhibitory proteinBeta-lactamase inhibitor protein
  • CarbapenemaseBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Beta-lactamase / Beta-lactamase inhibitor protein / protein-protein complex / BLIP / KPC-2 / Antibiotic resistance / Hydrolase / Plasmid / Secreted / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


regulation of beta-lactamase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region
Similarity search - Function
Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / BamE-like / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase ...Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / BamE-like / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase inhibitory protein / beta-lactamase / Carbapenem-hydrolyzing beta-lactamase KPC
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Streptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsHanes, M.S. / Jude, K.M. / Berger, J.M. / Kirsch, J.F. / Bonomo, R.A. / Handel, T.M.
CitationJournal: Biochemistry / Year: 2009
Title: Structural and biochemical characterization of the interaction between KPC-2 beta-lactamase and beta-lactamase inhibitor protein
Authors: Hanes, M.S. / Jude, K.M. / Berger, J.M. / Bonomo, R.A. / Handel, T.M.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbapenemase
B: Carbapenemase
C: Beta-lactamase inhibitory protein
D: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)91,2224
Polymers91,2224
Non-polymers00
Water12,647702
1
A: Carbapenemase
C: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)45,6112
Polymers45,6112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-10 kcal/mol
Surface area16430 Å2
MethodPISA
2
B: Carbapenemase
D: Beta-lactamase inhibitory protein


Theoretical massNumber of molelcules
Total (without water)45,6112
Polymers45,6112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-8 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.243, 66.391, 82.205
Angle α, β, γ (deg.)90.00, 101.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Carbapenemase / Beta-lactamase / Class A carbapenemase / Beta-lactamase / Class A carbapenemase KPC-2


Mass: 28054.275 Da / Num. of mol.: 2 / Fragment: UNP residues 30-293 / Mutation: G175S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPC-2, blaKPC-2 / Plasmid: pET24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q93LQ9, UniProt: Q9F663*PLUS, beta-lactamase
#2: Protein Beta-lactamase inhibitory protein / Beta-lactamase inhibitor protein / BLIP


Mass: 17556.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35804
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 8000, 6% ethylene glycol, 100mM citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 6, 2008
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.87→200 Å / Num. all: 71225 / Num. obs: 70092 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.084
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.463 / % possible all: 90.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å51.79 Å
Translation2.5 Å51.79 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→51.786 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.61 / σ(F): 0.06 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 3376 5.07 %
Rwork0.1688 --
obs0.1711 66546 93.27 %
all-71225 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.929 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 26.226 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å2-0 Å24.373 Å2
2---1.514 Å20 Å2
3----0.366 Å2
Refinement stepCycle: LAST / Resolution: 1.87→51.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6307 0 0 702 7009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086451
X-RAY DIFFRACTIONf_angle_d1.1248775
X-RAY DIFFRACTIONf_dihedral_angle_d17.1752236
X-RAY DIFFRACTIONf_chiral_restr0.074985
X-RAY DIFFRACTIONf_plane_restr0.0051139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.89350.32641090.25311916X-RAY DIFFRACTION69
1.8935-1.92180.2741010.2522185X-RAY DIFFRACTION78
1.9218-1.95180.31071240.23282311X-RAY DIFFRACTION81
1.9518-1.98380.28371310.21022398X-RAY DIFFRACTION87
1.9838-2.0180.25531520.19482538X-RAY DIFFRACTION91
2.018-2.05470.20771510.19172575X-RAY DIFFRACTION92
2.0547-2.09420.23381490.18262547X-RAY DIFFRACTION92
2.0942-2.1370.22251420.17242673X-RAY DIFFRACTION94
2.137-2.18340.23191270.16692642X-RAY DIFFRACTION95
2.1834-2.23420.22671240.16482680X-RAY DIFFRACTION95
2.2342-2.29010.22361540.17362611X-RAY DIFFRACTION93
2.2901-2.3520.22741140.17252695X-RAY DIFFRACTION95
2.352-2.42120.2291470.16572689X-RAY DIFFRACTION96
2.4212-2.49940.23011810.1672651X-RAY DIFFRACTION96
2.4994-2.58870.22121270.16542737X-RAY DIFFRACTION97
2.5887-2.69230.21271380.16362749X-RAY DIFFRACTION97
2.6923-2.81490.22491420.17212792X-RAY DIFFRACTION98
2.8149-2.96330.23031460.17562757X-RAY DIFFRACTION98
2.9633-3.14890.19381610.17392796X-RAY DIFFRACTION98
3.1489-3.3920.23481370.16872820X-RAY DIFFRACTION99
3.392-3.73320.19311360.15362835X-RAY DIFFRACTION99
3.7332-4.27320.17371720.13382799X-RAY DIFFRACTION100
4.2732-5.38290.1471620.12652847X-RAY DIFFRACTION100
5.3829-51.80590.17991490.15272927X-RAY DIFFRACTION99
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.1805-0.0301-0.0060.1003-0.01940.1299-0.0491-0.56070.08750.16080.04140.0362-0.04850.14450.04510.1802-0.0496-0.04130.2648-0.05310.084141.1329-10.7537-20.0553
20.13240.03660.06560.05250.08190.03010.1707-0.1720.1269-0.2210.11410.16290.0740.0862-0.00020.1728-0.01150.020.1374-0.00130.1182
30.4610.02250.1548-0.0655-0.00030.37660.0420.0460.02070.0106-0.0395-0.0098-0.00060.10190.08390.083-0.0133-0.00560.0948-0.00220.0594
40.2799-0.00470.1088-0.0071-0.12710.0315-0.19890.1765-0.0166-0.47060.0959-0.13330.4249-0.26230.00010.2292-0.0605-0.01160.1901-0.02450.1188
50.1755-0.11160.21630.2678-0.21560.0811-0.0063-0.0241-0.0008-0.01670.05440.03160.0833-0.11510.00210.1221-0.0302-0.00060.11220.00010.0785
60.0168-0.0936-0.02540.0623-0.02960.00240.18140.3479-0.2587-0.0766-0.1330.19780.02080.11270.00390.10150.0099-0.01450.1045-0.03730.0904
70.0065-0.14030-0.0020.12010.348-0.00660.0973-0.01040.07310.08250.02040.0170.07100.105-0.0008-0.00850.1537-0.00940.0904
80.31940.05050.02750.0826-0.14620.74220.0929-0.01570.02380.0646-0.0370.0592-0.10270.07230.21460.1066-0.00620.01290.0894-0.00190.07
90.53420.2344-0.2093-0.028-0.20120.29190.10240.01980.04470.0315-0.06420.0527-0.06250.06830.08520.1133-0.0010.0030.1086-0.0020.0629
100.37890.4473-0.08250.3977-0.02930.59290.1378-0.126-0.03520.15060.01340.3025-0.20430.11130.26240.1467-0.01260.04010.0996-0.00350.0838
110.04460.00660.00470.0311-00.0213-0.098-0.1936-0.17370.19690.20520.04940.2769-0.11550.00010.18690.009-0.02590.18920.04140.1446
120.0884-0.0445-0.0149-0.0618-0.05250.38190.1204-0.04570.07620.05210.03880.0094-0.11020.10920.38510.179-0.02020.0240.147-0.0170.0546
130.0204-0.0004-0.00170.01370.02270.00520.0531-0.01360.0080.4086-0.12220.1017-0.25450.0145-00.4104-0.04510.09040.1503-0.03890.1566
140.0024-0.0157-0.01380.0093-0.0319-0.0032-0.3335-0.2319-0.60780.7514-0.03050.42090.11690.0337-00.61580.00190.38630.27270.06670.4961
150.0073-0.0397-0.00040.0185-0.04630.02820.15310.1031-0.1561-0.19770.59920.28350.1149-0.20420.00040.2784-0.10020.0490.2627-0.02760.7288
160.0659-0.11120.13310.1444-0.09420.4139-0.16710.31290.07550.08640.26990.85760.0678-0.3059-0.02010.1444-0.0730.12150.2757-0.00790.6279
170.6449-0.490.13830.4520.00780.3605-0.3252-0.1017-0.1302-0.53310.52891.0216-0.1405-0.13410.09140.3159-0.2138-0.25210.1592-0.01870.2488
180.8933-0.11630.17470.1320.01560.1204-0.20860.40070.4601-0.7730.0509-0.2437-0.0288-0.1589-0.00910.5448-0.1507-0.02030.30740.08340.088
190.26020.0108-0.01270.2772-0.03980.0703-0.21450.0336-0.0181-0.19250.0775-0.05150.12610.11680.00010.1865-0.0399-0.01750.22290.02560.211
200.01970.01630.014-0.0074-0.0499-0.003-0.06370.12940.0723-0.89820.2340.32580.1561-0.13770.01060.2609-0.0727-0.26930.3930.10570.3241
21-0.00640.0287-0.00050.0046-0.0029-0.024-0.0450.1940.0698-0.18470.52230.76570.4189-0.21740.03620.2579-0.1577-0.31940.45250.03820.7839
220.01590.12060.02360.10460.08240.0237-0.00370.24410.55180.10280.30170.9960.1266-0.033800.14980.01520.02760.22390.08090.5783
230.066-0.00340.0020.01710.03140.03910.02410.11960.29760.05450.22430.36780.1698-0.65350.00030.1299-0.0256-0.06550.25450.09090.782
240.6946-0.4960.26790.38170.0048-0.0707-0.2171-0.4238-0.0638-0.51410.51370.8020.2589-0.14970.03710.338-0.1924-0.21630.1948-0.07870.4396
250.09640.0116-0.0610.1953-0.15720.055-0.2586-0.1066-0.2997-0.53790.1091-0.46610.13580.020300.3858-0.0870.08620.1658-0.05740.2652
260.12530.4583-0.57610.3268-0.52290.2607-0.0307-0.0341-0.15640.11110.02660.037-0.02240.070800.18340.0110.03150.17270.00780.3671
270.27750.4157-0.15310.2722-0.53060.3395-0.14890.0275-0.48150.15040.01520.6320.1737-0.1087-00.2018-0.04370.04420.1401-0.03080.4491
280.0078-0.01670.01060.01890.00150.00610.2623-0.30450.00660.58740.12730.219-0.12190.14310.00080.6075-0.08180.25790.3298-0.03280.3963
290.03860.00760.05260.0247-0.08880.1069-0.1216-0.1434-0.27680.3242-0.034-0.1425-0.04130.06650.00010.3237-0.00690.08090.24870.06310.3503
300.2140.03580.1467-0.02450.30820.35290.0184-0.1810.01960.076-0.13360.1012-0.051-0.20410.00020.12170.0052-0.01620.1394-0.03490.1263
310.04250.0344-0.00210.0215-0.0006-0.0073-0.22340.4494-0.04280.07040.185-0.0306-0.3912-0.2106-0.00870.13690.014-0.05040.18590.04440.0474
320.1001-0.0759-0.04930.009-0.05440.0426-0.0889-0.11540.0002-0.0657-0.03280.0332-0.0680.026-00.1115-0.017-0.02060.17880.01570.0997
330.02560.16470.00080.29540.07340.1976-0.03380.00940.1486-0.20210.03860.1631-0.09310.022100.1659-0.019-0.03880.13060.00160.1538
340.07770.02070.0650.08460.13180.1279-0.01940.06440.07340.26730.0958-0.17770.0460.25550.00140.14350.0588-0.03590.1338-0.01820.1386
350.0454-0.06050.1230.10180.02260.0381-0.193-0.01360.0312-0.00940.0916-0.150.302-0.0496-00.17070.03520.05190.1292-0.04880.3311
360.16010.0059-0.29290.4840.50170.145-0.18260.0287-0.0226-0.03530.1158-0.03510.04190.0034-00.1951-0.00620.00220.1068-0.02040.1519
370.00950.01430.02420.0025-0.0351-0.03630.18910.0411.02540.41190.3779-0.53920.28610.5853-0.00070.3902-0.0002-0.0580.4465-0.0820.7011
380.1787-0.1058-0.40860.41410.09570.324-0.2063-0.0675-0.0452-0.07010.2181-0.1769-0.0509-0.02170.01810.1115-0.00960.02250.0918-0.0530.1824
390.4101-0.0406-0.39260.01910.07830.297-0.0451-0.2239-0.1365-0.03870.0044-0.12970.09240.2596-00.1390.0187-0.01580.17580.00640.1975
400.2551-0.127-0.0140.17070.15060.0758-0.015-0.0471-0.2145-0.16220.0103-0.0390.1571-0.11110.00010.1483-0.0338-0.01090.22050.00170.2237
41-0.0386-0.09810.0303-0.0013-0.00270.11610.10450.0492-0.1256-0.0887-0.01-0.0706-0.11530.097-00.1269-0.00120.02620.1492-0.02020.1787
420.30040.11140.16780.1344-0.04560.55380.2925-0.02020.06220.26760.12270.3971-0.2437-0.05550.05420.23350.00140.08480.16850.01080.1954
430.21460.0239-0.07560.0064-0.01750.36910.053-0.05230.46150.76590.15611.0845-0.7430.0585-0.03240.36270.11160.17950.1371-0.0070.5908
440.05290.1102-0.05850.72-0.3274-0.16620.00830.0462-0.04970.13610.07740.1155-0.14020.0529-00.19-0.02440.00940.152-0.02260.1807
45-0.0042-0.0162-0.0092-0.00020.02140.0346-0.0548-0.43930.266-0.1053-0.19060.027-0.0583-0.2096-0.00030.58330.0160.28470.3161-0.02070.478
460.2577-0.09630.37430.5370.15730.5013-0.2981-0.12690.1504-0.08930.22080.74380.15320.1007-0.00020.13380.03290.02820.12190.05320.4353
Refinement TLS groupSelection details: chain D and resid 145:165)

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