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- PDB-6b2n: Crystal structure of TEM-1 beta-lactamase mutant M182N -

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Basic information

Entry
Database: PDB / ID: 6b2n
TitleCrystal structure of TEM-1 beta-lactamase mutant M182N
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / Antibiotic resistance / beta-lactamase
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJimah, J.R. / Tolia, N.H.
CitationJournal: ACS Cent Sci / Year: 2017
Title: Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models.
Authors: Zimmerman, M.I. / Hart, K.M. / Sibbald, C.A. / Frederick, T.E. / Jimah, J.R. / Knoverek, C.R. / Tolia, N.H. / Bowman, G.R.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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 1.2Oct 16, 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)116,0848
Polymers115,7004
Non-polymers3844
Water3,405189
1
A: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9251
Polymers28,9251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0212
Polymers28,9251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0212
Polymers28,9251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1173
Polymers28,9251
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.910, 49.660, 122.160
Angle α, β, γ (deg.)90.00, 90.10, 90.00
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: 28924.900 Da / Num. of mol.: 4 / Fragment: UNP residues 24-286 / Mutation: M182N
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M sodium phosphate dibasic/citric acid, pH 4.2, 0.1 M lithium sulfate, 20% PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 3, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 66091 / % possible obs: 98.6 % / Redundancy: 3.52 % / Rsym value: 0.099 / Net I/σ(I): 8.95
Reflection shellHighest resolution: 2 Å / Rsym value: 0.506

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JWP

1jwp


Resolution: 2→19.767 Å / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 31.92 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2828 1873 2.84 %
Rwork0.2307 --
obs0.2347 66017 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7998 0 20 189 8207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038138
X-RAY DIFFRACTIONf_angle_d0.58211009
X-RAY DIFFRACTIONf_dihedral_angle_d15.1864972
X-RAY DIFFRACTIONf_chiral_restr0.0391271
X-RAY DIFFRACTIONf_plane_restr0.0031420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05410.33461420.29584838X-RAY DIFFRACTION95
2.0541-2.11440.30271420.28474882X-RAY DIFFRACTION96
2.1144-2.18250.34791430.27314867X-RAY DIFFRACTION95
2.1825-2.26040.34311420.2784851X-RAY DIFFRACTION95
2.2604-2.35070.32241440.2674901X-RAY DIFFRACTION96
2.3507-2.45730.29491390.25624908X-RAY DIFFRACTION96
2.4573-2.58650.26191450.2584917X-RAY DIFFRACTION96
2.5865-2.74790.30151390.25424903X-RAY DIFFRACTION96
2.7479-2.95910.32011420.24544926X-RAY DIFFRACTION96
2.9591-3.25510.30961430.2324983X-RAY DIFFRACTION97
3.2551-3.72190.24261460.20174980X-RAY DIFFRACTION96
3.7219-4.67350.23981400.1715007X-RAY DIFFRACTION96
4.6735-17.1780.28571530.23395153X-RAY DIFFRACTION96
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)
10.0020.0068-0.00120.0237-0.00040.00670.01060.00280.009-0.02150.0112-0.0086-0.00310.00520.03020.2136-0.039-0.03920.02680.01760.0651-12.823421.7874-53.7288
20.00020.0010.00470.0027-0.00790.0152-0.0006-0.009-0.0162-0.00950.0035-0.00510.0360.00820.0010.3178-0.0055-0.0489-0.04670.0598-0.0078-22.46990.6705-49.2017
30.0023-0.00240.00270.0078-0.00720.00810.00250.005-0.0034-0.0044-0.00160.00420.0074-0.0039-0.00050.2199-0.0148-0.03590.0196-0.0356-0.0046-32.1324-7.4982-65.3949
40.00240.0007-0.00080.0027-0.00110.0014-0.00280.0026-0.0088-0.0019-0.00130.0020.00290.00210.00030.20440.0473-0.02540.0433-0.01230.0781-23.309-6.4488-59.4593
50.00330.00680.00470.00780.00360.0006-0.00540.02340.0116-0.0145-0.0198-0.0035-0.00460.0107-0.05810.4106-0.0133-0.0637-0.0743-0.0735-0.0101-22.55842.8436-50.1793
60.0059-0.00650.00210.0084-0.00220.00140.00430.0016-0.001-0.00090.00260.00020.0025-0.00210.00510.1949-0.0029-0.01290.02470.00110.0171-19.46628.1137-60.0662
70.0104-0.01070.0210.0086-0.02020.04730.02460.01070.0119-0.00220.0079-0.02290.00090.00120.07550.2146-0.0070.02750.0041-0.0419-0.0237-12.485413.5837-58.0296
80.0002-0.00030.00060.0005-0.0002-00.00260.00530.00080.0079-0.00460.0042-0.0039-0.000400.34060.022-0.02410.12940.04510.2759-29.78380.2241-22.8938
9-0.00230.00260.00180.01060.00390.00640.0024-0.0005-0.00180.0415-0.00470.01540.038-0.0040.00620.53410.0217-0.1269-0.08970.13720.025-16.6667-25.6757-26.1824
100.00320.00080.00360.00490.00170.00260.00870.00140.002-0.0045-0.0053-0.00510.00750.00090.00690.2619-0.0093-0.09210.0340.04590.0756-10.2928-15.0559-29.969
110.0014-0.0009-0.0010.00450.00030.0028-0.00280.0009-0.002-0.0033-0.00140.0052-0.0016-0.0018-0.00710.25920.0015-0.06980.03540.00850.0473-27.6111-26.4885-31.6602
12-0.0001-0.0002-0.0001-0-0.0001-0.0001-0.00080.0010.01320.00210.00170.0088-0.0015-0.005-0.00510.21470.03680.02670.07710.02330.0976-31.7662-19.8035-17.658
13-0.00020.00090.00020.0023-0.00250.0010.0005-0.0067-0.0057-0.01350.00120.02120.0039-0.0035-0.00390.2477-0.00160.01330.09250.07090.1252-26.8431-16.9983-21.3255
14-0.0001-00.00010-0.00050.00050.0003-0.0020.0066-0.00130.00570.0036-0.0019-0.007300.2267-0.0353-0.0060.11050.03130.1968-23.1319-10.0487-21.6252
150.0002-0.0001-0.0004-00.00030.00130.0030.00210.0013-0.0002-0.0010.0042-0.0025-0.0042-0.00240.16230.03960.03780.08010.0620.1606-32.2739-7.1963-18.386
160.00040.0001-0.00020.00010.00020.00010.0052-0.0018-0.0027-0.00970.00750.0018-0.0011-0.0038-00.182-0.061-0.01040.06420.00480.1133-28.7143-29.35195.1857
170.0478-0.0229-0.01990.01930.00060.02240.009-0.00090.0061-0.00390.0050.00140.0068-0.0080.02720.13210.00360.03820.018-0.01120.0228-29.3801-19.178514.2611
180.01490.0025-0.00490.01380.00040.02750.0018-0.0009-0.0020.00580.00760.004-0.01090.0010.02640.18920.01150.046-0.0106-0.00060.0177-17.1422-8.089812.5926
19-0.0028-0.00030.00050.0037-0.00080.02130.01530.00370.0171-0.0154-0.010.005-0.0217-0.0001-0.0010.4194-0.01180.0694-0.04270.05260.0033-11.40852.62595.1148
200.00430.0075-0.00670.0118-0.00930.0074-0.00020.0027-0.00280.0095-0.0144-0.01040.00960.0044-0.02910.2574-0.01440.07150.0028-0.00270.0008-13.7272-12.601213.4052
21-0.0024-0.00060.00080.00260.00180.0231-0.0060.0086-0.0086-0.00340.00240.006-0.0174-0.0068-0.01580.2410.01790.0251-0.00990.0331-0.0011-26.7703-8.87515.4231
220.00050.0003-0.0004-0.00030.00030.00020.00550.0051-0.00820.00350.0018-0.00180.0068-0.00420.00180.2244-0.066-0.0410.1233-0.01120.0671-29.9605-21.2323-0.0104
23-0.0011-0.0001-0.00110.002-0.00280.0001-0.0073-0.0053-0.0039-0.00250.00110.00140.0007-0.0078-0.01630.221-0.02570.0206-0.00630.04850.018214.0997-22.8429-33.037
24-0.0019-0.0001-0.00210.00530.00010.0018-0.0001-0.00040.0090.0197-0.0008-0.0009-0.01680.0039-0.00070.25740.02240.0771-0.05210.0739-0.012427.92024.4911-38.7718
250.00240.00390.00480.00530.00410.00370.00230.0037-0.0028-0.0098-0.0098-0.0066-0.00470-0.01480.18-0.00390.0595-0.02740.0088-0.012526.6897-0.6718-33.3188
260.00140.0017-0.00330.0016-0.00240.00510.00770.00370.00120.0032-0.0076-0.00140.00370.00310.00810.1907-00.09380.04660.03040.108831.2318-13.7028-31.2847
270.00230.00090.00440.00050.00190.0085-0.00660.0006-0.00010.0008-0.00290.00670.0046-0.0028-0.02350.14640.00230.02560.00720.0318-0.018316.0912-10.7428-26.9672
280.00160.00010.00030.0018-0.0010.00050.00010.00120.0054-0.0007-0.0050.00470.00260.0012-0.0040.2081-0.00680.02330.03660.06250.088412.30211.6968-32.0213
290.0006-0.0001-0.0020.0171-0.00350.00610.015-0.0026-0.0074-0.01260.00790.0160.0024-0.00530.00660.2009-0.04110.01510.04210.01290.06629.4499-11.262-45.6602
300.0002-0.0015-0.00040.0049-0.00170.00260.00560.00050.00050.00380.0090.01030.0087-0.00820.01150.137-0.00540.0240.01010.0420.066216.9662-12.0866-40.9149
310.00110.0028-0.00370.0106-0.01060.00920.01570.0010.01040.00460.01490.0209-0.0071-0.00990.0160.1809-0.0247-0.01180.04480.02940.081313.1149-16.2645-37.8889
320.0001-0.0004-0.00050.00010.0001-0.00020.0123-0.0053-0.003-0.01740.00140.01030.0076-0.0096-00.3688-0.0166-0.02960.1340.06230.155310.8924-21.6913-44.1523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 229 )
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 244 )
7X-RAY DIFFRACTION7chain 'A' and (resid 245 through 288 )
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 40 )
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 155 )
10X-RAY DIFFRACTION10chain 'B' and (resid 156 through 182 )
11X-RAY DIFFRACTION11chain 'B' and (resid 183 through 212 )
12X-RAY DIFFRACTION12chain 'B' and (resid 213 through 234 )
13X-RAY DIFFRACTION13chain 'B' and (resid 235 through 256 )
14X-RAY DIFFRACTION14chain 'B' and (resid 257 through 271 )
15X-RAY DIFFRACTION15chain 'B' and (resid 272 through 288 )
16X-RAY DIFFRACTION16chain 'C' and (resid 26 through 40 )
17X-RAY DIFFRACTION17chain 'C' and (resid 42 through 60 )
18X-RAY DIFFRACTION18chain 'C' and (resid 61 through 86 )
19X-RAY DIFFRACTION19chain 'C' and (resid 87 through 155 )
20X-RAY DIFFRACTION20chain 'C' and (resid 156 through 195 )
21X-RAY DIFFRACTION21chain 'C' and (resid 196 through 269 )
22X-RAY DIFFRACTION22chain 'C' and (resid 270 through 288 )
23X-RAY DIFFRACTION23chain 'D' and (resid 26 through 70 )
24X-RAY DIFFRACTION24chain 'D' and (resid 71 through 118 )
25X-RAY DIFFRACTION25chain 'D' and (resid 119 through 155 )
26X-RAY DIFFRACTION26chain 'D' and (resid 156 through 179 )
27X-RAY DIFFRACTION27chain 'D' and (resid 180 through 195 )
28X-RAY DIFFRACTION28chain 'D' and (resid 196 through 213 )
29X-RAY DIFFRACTION29chain 'D' and (resid 214 through 229 )
30X-RAY DIFFRACTION30chain 'D' and (resid 230 through 250 )
31X-RAY DIFFRACTION31chain 'D' and (resid 251 through 269 )
32X-RAY DIFFRACTION32chain 'D' and (resid 270 through 288 )

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