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- PDB-5kpu: Crystal structure of TEM1 beta-lactamase mutant I263L in the pres... -

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Basic information

Entry
Database: PDB / ID: 5kpu
TitleCrystal structure of TEM1 beta-lactamase mutant I263L in the presence of 1.2 MPa xenon
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / xenon
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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
XENON / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsRoose, B.W. / Dmochowski, I.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM097478 United States
Department of Defense Lung Cancer Research ProgramW81XWH-14-1-0424 United States
CitationJournal: Chemphyschem / Year: 2018
Title: A Structural Basis for129Xe Hyper-CEST Signal in TEM-1 beta-Lactamase.
Authors: Roose, B.W. / Zemerov, S.D. / Wang, Y. / Kasimova, M.A. / Carnevale, V. / Dmochowski, I.J.
History
DepositionJul 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase TEM
B: Beta-lactamase TEM
C: Beta-lactamase TEM
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,35417
Polymers115,6484
Non-polymers1,70713
Water21,6181200
1
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4375
Polymers28,9121
Non-polymers5254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3064
Polymers28,9121
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3064
Polymers28,9121
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3064
Polymers28,9121
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.430, 84.050, 95.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2


Mass: 28911.904 Da / Num. of mol.: 4 / Mutation: M182T, I263L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Plasmid: pJ411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62593, beta-lactamase
#2: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Xe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1200 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 2% (v/v) tacsimate (pH 6.0), 0.1 M BIS-TRIS (pH 6.5), 20% (w/v) PEG 3350
PH range: 6.0 - 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.181 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.45
ReflectionResolution: 1.5→43.65 Å / Num. obs: 148928 / % possible obs: 97.7 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.5-1.533.60.3610.904195.6
8.22-43.653.50.0380.997198.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.17data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HVI

5hvi


Resolution: 1.5→34.502 Å / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 22.82
RfactorNum. reflection% reflection
Rfree0.1926 15293 5.2 %
Rwork0.1698 --
obs0.1746 148867 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.35 Å2 / Biso mean: 10.7482 Å2 / Biso min: 2.92 Å2
Refinement stepCycle: final / Resolution: 1.5→34.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8051 0 12 1210 9273
Biso mean--13.94 19.21 -
Num. residues----1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088224
X-RAY DIFFRACTIONf_angle_d0.99311159
X-RAY DIFFRACTIONf_chiral_restr0.0481293
X-RAY DIFFRACTIONf_plane_restr0.0041457
X-RAY DIFFRACTIONf_dihedral_angle_d12.7343071
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52590.27677590.2455135761433591
1.5259-1.55360.286900.2425137981448891
1.5536-1.58350.25987050.2369137211442692
1.5835-1.61580.24557010.2221138761457791
1.6158-1.6510.23987460.2145137071445392
1.651-1.68940.21268190.2106137621458191
1.6894-1.73160.22647220.202138951461792
1.7316-1.77840.23847420.1971139371467992
1.7784-1.83070.21677480.1966139881473692
1.8307-1.88980.2067410.1885138251456693
1.8898-1.95730.22857700.1998140631483393
1.9573-2.03570.2077800.1874139591473993
2.0357-2.12830.21436710.1833141161478794
2.1283-2.24040.21336900.1805141361482694
2.2404-2.38070.19698000.1744140061480693
2.3807-2.56440.20197350.1585142311496694
2.5644-2.82220.1767720.1555141571492994
2.8222-3.230.16347380.1452142171495594
3.23-4.06720.14537790.1272142261500594
4.0672-26.73090.15428270.1437141791500694
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)
11.67251.02770.2714.2263-0.38361.48650.0036-0.18690.13330.102-0.04180.0221-0.1460.01610.01840.06070.0053-0.00940.0947-0.02810.045967.257523.611213.5728
21.374-0.46710.11982.31670.44881.3605-0.0232-0.09420.16870.05830.0192-0.0977-0.1490.1180.00610.0413-0.00530.01060.1206-0.01280.067276.66620.37989.8661
30.6345-0.1802-0.23920.36440.17571.2085-0.00050.0438-0.0645-0.0134-0.01150.03230.0755-0.0629-0.00110.0489-0.0006-0.00770.0323-0.00140.050973.37055.2593-14.5939
41.59930.04160.81971.0726-0.0461.68580.0001-0.001-0.0208-0.07620.0001-0.01980.00760.06070.00190.0322-0.00130.01410.0373-0.00630.033476.56216.5392-8.9448
52.31150.2157-0.29711.32130.381.62070.028-0.08320.00140.1474-0.06640.07130.1485-0.01370.03960.0551-0.0009-0.00330.0507-0.0020.046175.41923.6354.7247
60.5227-0.3337-0.54861.3958-1.6573.98180.1051-0.01070.06390.0057-0.0659-0.0738-0.24380.1556-0.0220.042-0.00990.00270.0841-0.01330.061480.462118.14541.8855
71.848-0.2193-1.08350.60450.14821.09850.040.00160.1128-0.02540.0027-0.0278-0.0934-0.0355-0.03250.05650.0029-0.00330.04870.00450.058672.410522.5929-8.3144
81.3383-0.0475-0.38941.1042-0.36341.2877-0.0082-0.0770.07570.0389-0.0039-0.0271-0.1012-0.03130.01320.03480.0056-0.00660.0578-0.01060.045665.63121.07063.6965
91.7451-1.08730.51613.40290.48080.6664-0.03420.10.0918-0.07180.0063-0.0497-0.03930.00370.02940.0394-0.00110.00210.07680.010.037299.212523.52568.9802
101.41340.04860.54361.801-0.3020.6166-0.02180.06010.1021-0.00290.05520.1024-0.0724-0.0883-0.00980.0380.00210.01780.09740.01260.066689.821420.29112.7705
110.7280.1953-0.00820.5275-0.24041.31310.033-0.0377-0.07160.0079-0.0318-0.04610.09880.0277-0.00440.0427-0.0038-0.00570.03-0.00060.060593.27255.326437.1928
120.4165-0.1255-0.04030.4261-0.231.04230.01870.0533-0.0107-0.0297-0.0034-0.02570.0873-0.0603-0.0150.0362-0.01270.00440.0502-0.00380.058289.39927.727324.5072
130.81770.207-0.40490.1902-0.11320.92170.01710.00750.04250.0151-0.00690.0116-0.05040.0411-0.01320.04030.00180.00030.0376-0.00120.051798.388121.574523.2252
142.88741.37561.34892.8850.08011.83050.06020.0487-0.03850.0753-0.0266-0.03980.15070.0174-0.03920.05890.01510.02220.0637-0.00430.032468.776910.00961.4052
151.2804-0.6288-0.10761.86550.03831.0317-0.0484-0.0009-0.0866-0.03040.01380.09590.1386-0.14040.03120.0624-0.01340.00310.087-0.00770.052459.353213.420257.4363
160.45970.35090.40450.57840.20130.5982-0.04520.06270.1107-0.0349-0.01170.0475-0.0730.03280.02410.04440.00260.00510.04180.00540.05357.489325.609834.3287
172.70730.4570.06012.28270.26181.5491-0.03590.05610.10120.07940.0819-0.1407-0.26490.1649-0.04290.0955-0.0362-0.00760.08360.00440.084470.975731.956131.2185
181.4719-0.3431-1.01450.5968-0.02832.2344-0.02730.061-0.0009-0.0230.0031-0.0106-0.0946-0.10450.01920.0468-0.009-0.01320.03770.0010.044359.255626.835838.9598
192.00720.95690.36451.67110.49570.9377-0.05510.00340.13130.10680.06710.0132-0.2244-0.0233-0.01930.11390.0124-0.01320.0376-0.00090.07561.334630.612852.5051
200.9663-0.80010.30131.84142.1114.81970.0895-0.072-0.0913-0.0096-0.10390.10880.1569-0.2073-00.0438-0.010.00340.06950.00780.040455.760815.528649.6279
212.0789-0.09210.93250.3938-0.20070.90610.01540.0246-0.105-0.02770.03580.02950.06150.0308-0.04540.0589-0.00530.00610.0403-0.00620.050263.891410.980239.5552
221.2490.08640.1421.01620.24651.270.0067-0.0858-0.0174-0.0418-0.0496-0.01630.0236-0.03550.05030.0319-0.0008-0.00030.03140.00980.049168.318614.483349.9282
233.73015.0609-0.11888.3499-0.12111.2615-0.03690.0089-0.10690.04350.0826-0.10470.2082-0.0298-0.03130.0760.0196-0.00220.08820.00150.046674.64288.69454.2666
241.1294-0.11860.43720.76670.23990.92010.0196-0.1001-0.10190.0442-0.0282-0.00380.2245-0.0820.00050.084-0.02410.01290.08050.00660.058179.4854-30.578437.2678
250.6360.27340.75830.40240.42760.9401-0.0227-0.03090.0681-0.0324-0.03240.028-0.0292-0.07230.01790.037-0.00090.0070.04540.00450.048772.3749-16.366211.8513
261.18180.93270.95452.47960.95282.9099-0.0077-0.00550.047-0.03990.0195-0.1648-0.13230.2366-0.00340.0557-0.0197-0.0040.11420.00610.080585.8855-10.42858.28
271.392-0.0609-0.81081.0646-0.13022.0406-0.0225-0.0004-0.02180.0066-0.0064-0.0018-0.0654-0.0920.02380.0379-0.0051-0.00960.043-0.00310.037374.2494-15.283516.4205
281.54960.14720.14671.50130.01561.2340.0012-0.06670.07970.0559-0.01430.0601-0.0814-0.11590.01130.04550.00530.00160.05390.00140.034174.208-16.900828.9955
292.52080.1750.60650.7647-0.05181.3940.01660.0178-0.134-0.01020.04660.01170.0362-0.072-0.04220.0593-0.01-0.0070.02810.00290.07870.8047-29.066513.8065
301.8160.55530.94830.60470.43891.60050.00090.0107-0.12030.0175-0.1414-0.06290.11770.13670.1070.04780.02440.02280.08440.00110.059287.7331-33.577820.8944
311.2422-0.08480.09890.6131-0.08210.90720.011-0.0275-0.04670.06050.010.00580.14290.0353-0.01320.06210.0006-0.00320.0444-0.00270.046585.307-29.663828.9951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 50 )A26 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 68 )A51 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 118 )A69 - 118
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 154 )A119 - 154
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 179 )A155 - 179
6X-RAY DIFFRACTION6chain 'A' and (resid 180 through 195 )A180 - 195
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 229 )A196 - 229
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 290 )A230 - 290
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 50 )B26 - 50
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 68 )B51 - 68
11X-RAY DIFFRACTION11chain 'B' and (resid 69 through 118 )B69 - 118
12X-RAY DIFFRACTION12chain 'B' and (resid 119 through 195 )B119 - 195
13X-RAY DIFFRACTION13chain 'B' and (resid 196 through 290 )B196 - 290
14X-RAY DIFFRACTION14chain 'C' and (resid 26 through 50 )C26 - 50
15X-RAY DIFFRACTION15chain 'C' and (resid 51 through 68 )C51 - 68
16X-RAY DIFFRACTION16chain 'C' and (resid 69 through 98 )C69 - 98
17X-RAY DIFFRACTION17chain 'C' and (resid 99 through 118 )C99 - 118
18X-RAY DIFFRACTION18chain 'C' and (resid 119 through 155 )C119 - 155
19X-RAY DIFFRACTION19chain 'C' and (resid 156 through 179 )C156 - 179
20X-RAY DIFFRACTION20chain 'C' and (resid 180 through 195 )C180 - 195
21X-RAY DIFFRACTION21chain 'C' and (resid 196 through 229 )C196 - 229
22X-RAY DIFFRACTION22chain 'C' and (resid 230 through 271 )C230 - 271
23X-RAY DIFFRACTION23chain 'C' and (resid 272 through 290 )C272 - 290
24X-RAY DIFFRACTION24chain 'D' and (resid 26 through 68 )D26 - 68
25X-RAY DIFFRACTION25chain 'D' and (resid 69 through 98 )D69 - 98
26X-RAY DIFFRACTION26chain 'D' and (resid 99 through 118 )D99 - 118
27X-RAY DIFFRACTION27chain 'D' and (resid 119 through 155 )D119 - 155
28X-RAY DIFFRACTION28chain 'D' and (resid 156 through 195 )D156 - 195
29X-RAY DIFFRACTION29chain 'D' and (resid 196 through 212 )D196 - 212
30X-RAY DIFFRACTION30chain 'D' and (resid 213 through 229 )D213 - 229
31X-RAY DIFFRACTION31chain 'D' and (resid 230 through 290 )D230 - 290

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