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- PDB-5i52: Crystal structure of TEM1 beta-lactamase mutant I263N -

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Basic information

Entry
Database: PDB / ID: 5i52
TitleCrystal structure of TEM1 beta-lactamase mutant I263N
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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
DepositionFeb 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 16, 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 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 1.5Nov 6, 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


Theoretical massNumber of molelcules
Total (without water)115,6514
Polymers115,6514
Non-polymers00
Water14,520806
1
A: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9131
Polymers28,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9131
Polymers28,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9131
Polymers28,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9131
Polymers28,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.987, 83.509, 95.784
Angle α, β, γ (deg.)90.000, 90.060, 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: 28912.846 Da / Num. of mol.: 4 / Mutation: M180T, I259N
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate (pH 7.0), 20% (w/v) PEG 3350 / PH range: 7.0 - 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: 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: 0.21
ReflectionResolution: 1.75→95.78 Å / Num. obs: 93490 / % possible obs: 98.3 % / Redundancy: 6.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.154 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.75-1.786.60.807197.7
9.59-95.787.10.06199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5hvi


Resolution: 1.75→62.945 Å / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 30.35
RfactorNum. reflection% reflection
Rfree0.2178 9301 5.05 %
Rwork0.174 --
obs0.1759 93461 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.29 Å2 / Biso mean: 14.8561 Å2 / Biso min: 5.27 Å2
Refinement stepCycle: final / Resolution: 1.75→62.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8019 0 0 806 8825
Biso mean---23.83 -
Num. residues----1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078187
X-RAY DIFFRACTIONf_angle_d1.06311114
X-RAY DIFFRACTIONf_chiral_restr0.0411288
X-RAY DIFFRACTIONf_plane_restr0.0051454
X-RAY DIFFRACTIONf_dihedral_angle_d13.0513042
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 (%)
1.7502-1.78030.32984710.28728709918093
1.7803-1.81250.3454790.27618559903892
1.8125-1.84730.33134410.25168660910193
1.8473-1.88490.27484750.22298680915593
1.8849-1.92570.26884230.2078794921794
1.9257-1.97040.26745200.19878606912693
1.9704-2.01950.23314220.19228806922894
2.0195-2.07380.24684130.19368745915894
2.0738-2.13460.21055420.18128772931493
2.1346-2.20310.23943530.17888601895493
2.2031-2.28140.21694530.17818747920094
2.2814-2.37220.23184350.16948837927294
2.3722-2.47930.19424020.17068846924895
2.4793-2.6090.19255460.16578825937193
2.609-2.77080.21654170.16778748916594
2.7708-2.98210.21124570.16398666912393
2.9821-3.27740.23825000.15538774927494
3.2774-3.74070.19164350.1348879931495
3.7407-4.67250.1494790.12798684916393
4.6725-12.58940.17464900.1638703919393
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)
11.37050.0221-0.72591.2761-0.17281.11230.0732-0.05010.09570.0706-0.02190.0347-0.09670.0655-0.07180.10770.01760.07110.21-0.02460.11027.039923.6575109.3248
20.85220.2445-0.23430.2756-0.58241.3550.0984-0.01670.08360.0756-0.0595-0.0268-0.21290.0828-0.08910.12170.00450.08880.1802-0.00290.129716.30520.2907105.856
30.73060.3818-0.36570.6622-0.06111.9207-0.06690.0573-0.136-0.03530.02350.02450.2299-0.170.04830.1144-0.01690.06680.1051-0.00890.117912.93115.609481.2714
41.8633-0.2433-0.29521.10850.28840.889-0.03810.05950.055-0.09750.0205-0.00210.0385-0.0144-0.02180.0792-0.01930.05650.12730.00790.08911.74717.154383.5319
51.89050.2262-0.13650.46950.16811.5563-0.0457-0.0754-0.1410.0724-0.00850.04070.12640.04040.04370.1194-0.00210.090.11520.0070.12417.68874.255298.5804
60.42390.0537-0.35320.1552-0.21550.80170.02910.01220.0747-0.0298-0.0138-0.0672-0.07490.11980.02380.0989-0.0180.08160.147-0.00490.107919.922119.510990.3535
71.24970.1062-0.48040.7215-0.20541.27390.03570.03150.07890.0316-0.02830.0502-0.0699-0.0242-0.06840.07420.00580.06290.1616-0.00050.07226.201520.957596.1567
83.24362.3773-1.5462.7137-1.3251.88190.1662-0.0760.19740.2602-0.12350.2567-0.16770.0523-0.0610.11370.04280.05230.21750.00030.09441.278725.0592102.2429
90.50720.00060.00250.29950.01720.38680.01120.020.0371-0.021-0.02320.0031-0.0577-0.0246-0.10490.0962-0.00350.09390.17980.00830.107534.244522.1969106.5762
101.3885-0.19-0.50640.43-0.11972.0259-0.0584-0.1265-0.15110.02870.0143-0.01470.20970.17230.07250.12180.00840.08030.1126-0.00470.114532.4465.2853133.0573
110.82780.0395-0.01450.2441-0.22220.95120.0010.0361-0.0205-0.0388-0.0108-0.01250.1306-0.00140.02170.10550.00580.10220.0923-00.090828.90587.7555120.3962
123.513-0.066-1.42871.0412-0.19212.03320.09870.01860.23390.10480.05480.201-0.1838-0.0977-0.12970.1219-0.00150.08660.06870.01160.13925.420820.4971130.0178
130.76290.0047-0.19860.3445-0.06330.50470.02930.00210.0434-0.0204-0.0178-0.0467-0.02190.0389-0.0240.0755-0.00710.08160.158-0.00650.092739.143220.7631118.1359
142.7174-2.432-1.28554.39040.86771.54920.05370.02890.0522-0.1117-0.0665-0.0888-0.0324-0.0015-0.0080.0882-0.04090.04860.202-0.0020.08544.133124.8326112.0198
152.47060.0118-0.50510.5006-0.00890.8252-0.0581-0.1179-0.17110.05330.0147-0.01170.09080.1130.04070.09340.02190.0690.12640.0090.10037.804510.1245157.1485
160.40980.0027-0.00330.0971-0.0680.6458-0.01820.01330.0161-0.010.0097-0.00940.0171-0.04460.01490.0997-0.01150.10370.0612-0.00420.1145-2.37620.7207139.204
171.03140.1661-0.43360.6559-0.36951.49460.02430.09560.0323-0.0077-0.0239-0.0561-0.11630.0691-0.01110.1011-0.01630.07840.09710.00260.09033.08328.5095131.9592
181.52360.81790.41741.1572-0.22930.5121-0.01230.00580.11040.04960.0618-0.0265-0.17150.008-0.03490.152-0.00370.07650.0536-0.00120.15020.917230.575148.3351
190.4986-0.293-0.35880.99661.41163.6871-0.01160.0236-0.0674-0.049-0.09950.02410.1478-0.19080.14520.1009-0.00240.06240.0838-0.00630.0797-4.835715.7236145.6748
202.49551.26911.37162.106-0.52192.05080.0003-0.0651-0.00430.01850.0770.24010.1073-0.1785-0.0520.1466-0.01850.07590.06270.00110.109-4.595612.9185132.1868
210.8523-0.0449-0.44630.21730.13171.0785-0.02950.0113-0.033-0.02480.033-0.05720.04760.1127-0.03450.10760.0150.08770.08160.00380.09089.117312.6862143.9374
222.43311.637-0.43883.82931.17641.24950.0079-0.1679-0.09240.0775-0.07-0.06950.13450.09730.06940.10890.04150.05660.17590.02290.080213.83918.7233150.2625
231.6880.8384-0.2071.45980.36221.07850.0171-0.1684-0.14230.0941-0.0874-0.07020.0992-0.02430.07470.09770.00240.0720.14990.02110.105322.5058-31.8094134.5551
240.86530.1176-0.47280.5415-0.03391.1057-0.0863-0.0442-0.09470.0519-0.00020.05040.2187-0.08480.09390.1121-0.00040.07490.1463-0.00120.110713.1478-28.5664130.7496
250.7624-0.3683-0.12960.2645-0.29591.5959-0.01880.06210.05890.0425-0.0416-0.0162-0.16610.120.00120.1156-0.0210.0710.1099-0.00170.099417.2338-13.8045106.143
260.5862-0.0267-0.22060.1512-0.01590.8067-0.02520.0079-0.0569-0.01510-0.010.03170.00010.00330.0936-0.00750.08140.0876-0.00440.092618.203-15.4042108.5426
274.07582.2826-2.08451.7124-1.19471.94520.00920.1760.08820.03870.02640.2042-0.0131-0.2406-0.03970.08930.02750.05640.19270.00740.10965.0963-14.2426118.8623
281.18030.3278-0.24560.418-0.18451.47650.06240.02130.08440.0719-0.00920.0495-0.106-0.0488-0.04410.0987-0.00320.0710.07020.01180.101613.5504-16.6059124.7349
292.33160.03921.00591.03390.1982.2457-0.0382-0.0174-0.28560.04520.04940.16460.1856-0.15720.01880.1247-0.01040.0720.0692-0.00030.124810.0756-28.9121109.4478
301.38270.2053-0.44020.2438-0.02411.3576-0.0223-0.0531-0.084-0.0038-0.0001-0.05630.07640.08240.01950.09590.00660.07590.07040.00660.088223.6136-29.0911121.4038
312.48641.13750.15523.22291.41191.201-0.0497-0.1115-0.12230.0358-0.0171-0.06970.12340.06460.05840.08880.02590.06280.14820.01910.085928.5392-33.1881127.5475
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 142 )A119 - 142
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 179 )A143 - 179
6X-RAY DIFFRACTION6chain 'A' and (resid 180 through 212 )A180 - 212
7X-RAY DIFFRACTION7chain 'A' and (resid 213 through 271 )A213 - 271
8X-RAY DIFFRACTION8chain 'A' and (resid 272 through 290 )A272 - 290
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 68 )B26 - 68
10X-RAY DIFFRACTION10chain 'B' and (resid 69 through 118 )B69 - 118
11X-RAY DIFFRACTION11chain 'B' and (resid 119 through 195 )B119 - 195
12X-RAY DIFFRACTION12chain 'B' and (resid 196 through 212 )B196 - 212
13X-RAY DIFFRACTION13chain 'B' and (resid 213 through 271 )B213 - 271
14X-RAY DIFFRACTION14chain 'B' and (resid 272 through 290 )B272 - 290
15X-RAY DIFFRACTION15chain 'C' and (resid 26 through 50 )C26 - 50
16X-RAY DIFFRACTION16chain 'C' and (resid 51 through 98 )C51 - 98
17X-RAY DIFFRACTION17chain 'C' and (resid 99 through 155 )C99 - 155
18X-RAY DIFFRACTION18chain 'C' and (resid 156 through 179 )C156 - 179
19X-RAY DIFFRACTION19chain 'C' and (resid 180 through 195 )C180 - 195
20X-RAY DIFFRACTION20chain 'C' and (resid 196 through 212 )C196 - 212
21X-RAY DIFFRACTION21chain 'C' and (resid 213 through 271 )C213 - 271
22X-RAY DIFFRACTION22chain 'C' and (resid 272 through 290 )C272 - 290
23X-RAY DIFFRACTION23chain 'D' and (resid 26 through 50 )D26 - 50
24X-RAY DIFFRACTION24chain 'D' and (resid 51 through 68 )D51 - 68
25X-RAY DIFFRACTION25chain 'D' and (resid 69 through 118 )D69 - 118
26X-RAY DIFFRACTION26chain 'D' and (resid 119 through 142 )D119 - 142
27X-RAY DIFFRACTION27chain 'D' and (resid 143 through 155 )D143 - 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 271 )D213 - 271
31X-RAY DIFFRACTION31chain 'D' and (resid 272 through 290 )D272 - 290

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