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- PDB-6ayk: Crystal structure of TEM1 beta-lactamase mutant I263A in the pres... -

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Basic information

Entry
Database: PDB / ID: 6ayk
TitleCrystal structure of TEM1 beta-lactamase mutant I263A in the presence of 1.2 MPa xenon
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / Enzyme / 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 / Resolution: 1.44 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 (DOD, United States)W81XWH-14-1-0424 United States
CitationJournal: Chemphyschem / Year: 2019
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
DepositionSep 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: 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 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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

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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)117,31718
Polymers115,4794
Non-polymers1,83814
Water18,2671014
1
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2644
Polymers28,8701
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2644
Polymers28,8701
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2644
Polymers28,8701
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5266
Polymers28,8701
Non-polymers6565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.645, 84.751, 95.971
Angle α, β, γ (deg.)90.000, 90.230, 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: 28869.822 Da / Num. of mol.: 4 / Fragment: UNP residues 24-286 / Mutation: M182T, I263A
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62593, beta-lactamase
#2: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Xe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1014 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 2% v/v Tacsimate, pH 6.0, 0.1 M Bis-Tris, pH 6.5, 20% w/v PEG3350
PH range: 6.0-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2017
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.07
ReflectionResolution: 1.44→95.97 Å / Num. obs: 174485 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.061 / Rrim(I) all: 0.159 / Net I/σ(I): 7.5 / Num. measured all: 1138030 / Scaling rejects: 1178
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.44-1.466.11.22385660.6570.5341.33899.3
7.89-95.976.50.06711300.9960.0280.07399.7

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5HVI

5hvi


Resolution: 1.44→95.97 Å / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 30.28
RfactorNum. reflection% reflection
Rfree0.2191 17405 5.05 %
Rwork0.1972 --
obs0.1983 174454 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.39 Å2 / Biso mean: 15.7069 Å2 / Biso min: 6.21 Å2
Refinement stepCycle: final / Resolution: 1.44→95.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7970 0 11 1015 8996
Biso mean--17.75 28.16 -
Num. residues----1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068141
X-RAY DIFFRACTIONf_angle_d1.05111056
X-RAY DIFFRACTIONf_chiral_restr0.0691290
X-RAY DIFFRACTIONf_plane_restr0.0041440
X-RAY DIFFRACTIONf_dihedral_angle_d11.893010
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4401-1.4650.37198450.3529162741711994
1.465-1.49160.35047860.3322164511723795
1.4916-1.52030.35138260.3032163871721395
1.5203-1.55130.30579100.2962163221723294
1.5513-1.58510.26997760.2722163931716995
1.5851-1.62190.29068890.2553163641725394
1.6219-1.66250.26439450.2398163131725894
1.6625-1.70740.25617480.2345164771722595
1.7074-1.75770.22979240.2262162221714694
1.7577-1.81440.22279100.2185163681727894
1.8144-1.87930.20428260.2138164291725595
1.8793-1.95450.22398630.2003163641722795
1.9545-2.04350.21027900.1957164391722995
2.0435-2.15120.208710100.19162511726194
2.1512-2.2860.19149380.1792162871722594
2.286-2.46250.28640.1809163851724995
2.4625-2.71020.22199360.1781162771721394
2.7102-3.10230.18929010.1749163341723594
3.1023-3.90810.1787880.1514164491723795
3.9081-42.39380.19298110.1555163451715694
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)
11.89832.13430.26514.84250.63751.80760.1412-0.1891-0.16030.1557-0.0946-0.20090.2687-0.0886-0.05120.1459-0.0114-0.01920.14040.02860.085123.3393-24.171513.0194
20.63980.1233-0.78073.73930.79031.4332-0.0346-0.0194-0.01510.0846-0.05410.1850.22-0.25860.09640.139-0.0419-0.03760.17020.02360.105913.8365-20.54689.4443
31.72420.09010.08290.6710.00280.7515-0.03710.13620.1017-0.04510.0187-0.0127-0.05880.00760.01380.12160.0048-0.01350.05820.00030.087517.1294-6.1198-14.9267
42.10160.2579-0.81480.5042-0.50342.3782-0.03350.0236-0.0322-0.02810.0294-0.0035-0.0071-0.1149-0.00520.09410.0034-0.02180.0417-0.0060.08113.7921-7.4704-9.0555
53.78141.22611.55941.08970.39520.71070.0196-0.2685-0.00040.1359-0.0688-0.0352-0.0782-0.060.04040.14080.0149-0.00750.0927-0.01110.089915.7986-3.87344.6852
61.99881.28881.84554.91195.26937.14450.101-0.1855-0.1264-0.0359-0.14970.10020.1514-0.37510.07160.0956-0.0136-0.02380.11170.02080.099410.4677-18.77931.4825
75.31670.03532.58411.9984-0.30331.88050.0767-0.2695-0.1628-0.0672-0.00480.08220.1125-0.2145-0.02920.1303-0.0023-0.02130.0628-0.00570.085810.4651-21.1472-11.9967
82.73771.44861.29147.6189-1.20152.52410.0938-0.0041-0.17860.2502-0.1786-0.35520.14680.03410.08560.11540.02490.00290.0872-0.010.085227.4455-25.5346-4.9286
91.4914-0.03740.16280.8480.31251.31940.037-0.1278-0.09610.0428-0.0464-0.02610.1418-0.00020.03350.11630.0016-0.02520.06360.00680.073322.7966-19.6341.8488
104.62634.5378-1.00856.7212-1.08321.99570.0054-0.1571-0.21720.01330.0127-0.21050.29780.094-0.00080.16890.0304-0.03190.12210.01440.092128.949-25.56075.9786
112.4288-1.32690.18394.7221-0.17972.30190.04410.2916-0.1248-0.1946-0.06270.17440.0956-0.01740.00020.1062-0.005-0.01380.1243-0.02770.0756-8.6506-24.28738.8453
121.2487-0.83030.23372.8228-1.19162.1330.08420.2213-0.1272-0.2269-0.0688-0.03080.23890.1442-0.01340.1028-0.0073-0.02110.1239-0.0290.10280.7286-20.75812.3662
130.90930.09540.18930.58140.00930.79810.0047-0.05950.09350.0454-0.01160.0471-0.0564-0.0489-0.00860.12260.0044-0.00310.0345-0.00210.1112-3.0086-7.058536.8232
141.2378-0.46820.41731.08790.5391.1768-0.03930.2170.1749-0.13820.0356-0.0136-0.18340.1636-0.02760.1532-0.0247-0.02410.05570.02650.1131.7796-4.379722.3058
150.8348-0.3810.22154.1942-3.51554.94130.00810.1054-0.1054-0.03070.02-0.08690.18340.0691-0.02240.08610.0056-0.02240.0505-0.01730.09894.5901-18.801320.5676
161.50910.31190.31130.43390.01890.766-0.0102-0.0468-0.11370.00840.0176-0.04240.0019-0.0348-0.01130.1279-0.0005-0.0160.0390.00630.1029-3.4636-23.17530.6418
171.1730.12680.02640.9897-0.29611.2957-0.02640.1224-0.08870.02840.0181-0.00470.0285-0.05840.04140.10770.0032-0.02570.05-0.00820.0943-7.8962-19.945120.3476
183.2489-3.4763-0.49887.991.34932.7790.04090.1423-0.1119-0.1245-0.05680.14250.127-0.11520.00770.0858-0.0298-0.020.104-0.00750.0835-14.1945-25.490116.0964
194.12392.9207-0.5845.0435-0.38391.33470.0893-0.06080.19280.1334-0.09440.1484-0.2888-0.17240.00610.1520.0195-0.03680.0856-0.010.079221.8181-10.676761.1052
201.14651.0503-0.22284.774-1.61012.9817-0.0088-0.01680.09220.2626-0.0530.0091-0.30740.28780.05860.109-0.0113-0.03060.1215-0.00760.089431.1083-14.136757.5213
210.9868-0.0498-0.08420.46580.10240.7187-0.0220.0998-0.03920.00720.01720.02370.0827-0.0020.00260.1302-0.0078-0.02310.0356-0.0050.100729.3141-28.174735.2972
221.57780.26790.05351.39160.4361.49890.0037-0.1259-0.09860.16090.0326-0.02290.20460.0036-0.01650.13280.0158-0.01710.06060.00750.086331.2742-25.60551.3082
230.7263-0.1076-0.35690.44150.03430.5639-0.0074-0.01880.1428-0.01710.0255-0.045-0.0778-0.0139-0.03180.1465-0.0017-0.02540.02510.00760.128826.7323-11.486339.4833
241.1173-0.14350.08360.146-0.2921.2336-0.0347-0.1140.05790.0159-0.0665-0.0232-0.1382-0.0579-0.06220.1521-0.0079-0.02610.0317-0.00750.100222.36-15.022849.6671
254.39274.37390.37617.4104-0.1670.6356-0.0597-0.20840.25280.38060.07920.2765-0.4584-0.3649-0.01710.25440.0657-0.02970.1599-0.01620.10816.0575-9.292354.0411
263.59741.811-0.87973.4778-0.69851.2348-0.0105-0.20520.17050.1117-0.04260.1069-0.2476-0.03260.03140.1459-0.0079-0.04080.0986-0.0170.07976.855331.711339.2375
270.45990.46910.13771.8089-0.04110.068-0.0184-0.05250.06210.1184-0.047-0.0134-0.19150.0851-0.03050.1875-0.033-0.02940.0549-0.01120.128516.646328.681935.4263
280.5935-0.2559-0.54390.5689-0.06110.68550.0021-0.00590.0076-0.0417-0.0131-0.02120.06720.03020.0110.1212-0.0119-0.02960.0434-0.00570.092418.357816.236312.2601
291.7540.9757-1.55152.23750.94893.308-0.17210.317-0.0983-0.05270.02120.1890.3465-0.42970.16020.1374-0.0363-0.02060.1433-0.01750.13024.905510.49628.6976
302.3230.12681.03120.32010.41131.9656-0.02170.0156-0.0210.0075-0.0067-0.00630.0572-0.00390.02550.1125-0.0061-0.01220.0310.00580.082516.443515.158116.825
311.9720.9147-1.2381.2531-0.19271.0373-0.0232-0.1813-0.04720.1627-0.04560.02710.20710.1170.06220.15440.0147-0.010.05990.01230.104314.208211.32730.4793
320.94231.2371-1.34163.4299-2.57653.38370.0104-0.0767-0.0010.0006-0.0715-0.2003-0.04570.20680.0490.1233-0.0175-0.01820.0354-0.00940.113420.008926.274127.4875
332.3444-0.6216-0.94880.37580.31691.2330.02620.06980.0873-0.029-0.0069-0.0456-0.0883-0.0995-0.01470.1205-0.0003-0.02030.03970.00340.097411.948431.011917.5976
340.9812-0.051-0.02050.20690.19730.7354-0.0052-0.06420.06230.0457-0.03140.025-0.0977-0.0434-0.08260.1483-0.0218-0.03180.01250.00150.10857.514727.465427.8514
353.67142.98971.05342.76391.07582.68540.0319-0.12840.12970.2580.05750.0459-0.1952-0.1048-0.05880.12110.041-0.00510.1092-0.01210.10921.542833.36132.1401
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 155 )A119 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 179 )A156 - 179
6X-RAY DIFFRACTION6chain 'A' and (resid 180 through 195 )A180 - 195
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 212 )A196 - 212
8X-RAY DIFFRACTION8chain 'A' and (resid 213 through 229 )A213 - 229
9X-RAY DIFFRACTION9chain 'A' and (resid 230 through 271 )A230 - 271
10X-RAY DIFFRACTION10chain 'A' and (resid 272 through 290 )A272 - 290
11X-RAY DIFFRACTION11chain 'B' and (resid 26 through 50 )B26 - 50
12X-RAY DIFFRACTION12chain 'B' and (resid 51 through 68 )B51 - 68
13X-RAY DIFFRACTION13chain 'B' and (resid 69 through 131 )B69 - 131
14X-RAY DIFFRACTION14chain 'B' and (resid 132 through 179 )B132 - 179
15X-RAY DIFFRACTION15chain 'B' and (resid 180 through 195 )B180 - 195
16X-RAY DIFFRACTION16chain 'B' and (resid 196 through 229 )B196 - 229
17X-RAY DIFFRACTION17chain 'B' and (resid 230 through 271 )B230 - 271
18X-RAY DIFFRACTION18chain 'B' and (resid 272 through 290 )B272 - 290
19X-RAY DIFFRACTION19chain 'C' and (resid 26 through 50 )C26 - 50
20X-RAY DIFFRACTION20chain 'C' and (resid 51 through 68 )C51 - 68
21X-RAY DIFFRACTION21chain 'C' and (resid 69 through 155 )C69 - 155
22X-RAY DIFFRACTION22chain 'C' and (resid 156 through 195 )C156 - 195
23X-RAY DIFFRACTION23chain 'C' and (resid 196 through 229 )C196 - 229
24X-RAY DIFFRACTION24chain 'C' and (resid 230 through 271 )C230 - 271
25X-RAY DIFFRACTION25chain 'C' and (resid 272 through 290 )C272 - 290
26X-RAY DIFFRACTION26chain 'D' and (resid 26 through 50 )D26 - 50
27X-RAY DIFFRACTION27chain 'D' and (resid 51 through 68 )D51 - 68
28X-RAY DIFFRACTION28chain 'D' and (resid 69 through 98 )D69 - 98
29X-RAY DIFFRACTION29chain 'D' and (resid 99 through 118 )D99 - 118
30X-RAY DIFFRACTION30chain 'D' and (resid 119 through 155 )D119 - 155
31X-RAY DIFFRACTION31chain 'D' and (resid 156 through 179 )D156 - 179
32X-RAY DIFFRACTION32chain 'D' and (resid 180 through 195 )D180 - 195
33X-RAY DIFFRACTION33chain 'D' and (resid 196 through 229 )D196 - 229
34X-RAY DIFFRACTION34chain 'D' and (resid 230 through 271 )D230 - 271
35X-RAY DIFFRACTION35chain 'D' and (resid 272 through 290 )D272 - 290

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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