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- PDB-6apa: Crystal structure of TEM1 beta-lactamase mutant I263A -

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Basic information

Entry
Database: PDB / ID: 6apa
TitleCrystal structure of TEM1 beta-lactamase mutant I263A
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / Enzyme
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: 1.86 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
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 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 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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


Theoretical massNumber of molelcules
Total (without water)115,4794
Polymers115,4794
Non-polymers00
Water18,3571019
1
A: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,8701
Polymers28,8701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,8701
Polymers28,8701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,8701
Polymers28,8701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,8701
Polymers28,8701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.669, 84.292, 95.914
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: 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1019 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
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: ADSC QUANTUM 315 / Detector: CCD / 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: 0.46
ReflectionResolution: 1.86→95.91 Å / Num. obs: 79520 / % possible obs: 98.2 % / Redundancy: 6.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.068 / Rrim(I) all: 0.176 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.86-1.96.40.50244700.9360.2150.54797.4
9.48-95.916.80.076480.9980.0290.07699.5

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Processing

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

5hvi


Resolution: 1.86→95.91 Å / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 31.94
RfactorNum. reflection% reflection
Rfree0.2489 4025 5.18 %
Rwork0.2132 --
obs0.2148 79479 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.38 Å2 / Biso mean: 11.6461 Å2 / Biso min: 2.79 Å2
Refinement stepCycle: final / Resolution: 1.86→95.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7993 0 0 1072 9065
Biso mean---17.29 -
Num. residues----1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028169
X-RAY DIFFRACTIONf_angle_d0.61311093
X-RAY DIFFRACTIONf_chiral_restr0.0241291
X-RAY DIFFRACTIONf_plane_restr0.0041447
X-RAY DIFFRACTIONf_dihedral_angle_d11.793033
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 (%)
1.8602-1.89230.32133630.26567443780693
1.8923-1.92670.32033820.26667234761692
1.9267-1.96370.28134120.25497493790592
1.9637-2.00380.26984000.24177318771893
2.0038-2.04730.26384010.23527387778893
2.0473-2.09490.27123480.23727456780493
2.0949-2.14720.24033940.22737401779593
2.1472-2.20520.28174240.2237448787293
2.2052-2.27010.23434110.22667364777593
2.2701-2.34330.30183670.2237491785894
2.3433-2.42690.28574090.22047434784393
2.4269-2.52390.26654340.21727493792793
2.5239-2.63860.22414420.21017333777593
2.6386-2.77740.27863940.21967315770992
2.7774-2.95110.26563540.20537545789995
2.9511-3.17820.2423480.20147537788595
3.1782-3.49690.2384030.18897481788494
3.4969-4.00010.19394640.17447508797293
4.0001-5.02910.18464120.1717445785794
5.0291-21.55970.24953860.23377413779993
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)
10.5924-0.42520.35220.59790.18151.16330.0121-0.1606-0.12230.0169-0.06070.02630.2171-0.04590.03510.09190.0040.00280.07570.03520.146419.2138-22.879211.3693
20.315-0.08240.14650.14090.12160.3643-0.01190.06560.1324-0.00330.0008-0.0449-0.12920.06890.01780.0879-0.0058-0.01320.01860.00670.110217.1764-5.9414-15.0832
30.28590.1002-0.21790.453-0.23390.9719-0.0241-0.02570.05260.0806-0.0030.02460.00470.0160.02510.0690.00090.00070.0295-0.00710.109414.6617-5.945-3.2504
40.5754-0.0778-0.02180.65150.02220.7962-0.0037-0.1228-0.13190.01350.0295-0.02240.09340.0405-0.01880.05350.0028-0.01280.03850.00110.099720.6365-21.8509-0.8877
50.4718-0.0471-0.18080.5457-0.15430.7322-0.01810.1901-0.1134-0.0123-0.02260.01420.1709-0.00650.02850.0878-0.0126-0.01360.0704-0.02320.1578-4.5491-22.858710.3839
60.14910.03580.0290.1122-0.04530.18470.0049-0.02590.11420.04060.0010.051-0.0978-0.02760.04320.10510.00260.0091-0.00260.00080.1314-2.3391-5.677936.9698
70.53310.3054-0.31830.45860.11770.6173-0.03980.07870.0558-0.06060.0147-0.0218-0.0712-0.04490.00910.0734-0.008-0.00860.02460.0060.1050.4398-5.855125.1721
80.37140.1512-0.01590.3758-0.00320.2694-0.0070.0708-0.1259-0.01130.0576-0.02620.04980.0106-0.02220.05590.0089-0.01870.0186-0.00740.1242-3.6784-20.948824.4662
91.47060.10861.04650.1028-0.17111.39420.11810.2286-0.1498-0.1255-0.0620.17490.12980.0593-0.05120.0484-0.0255-0.02410.1321-0.00690.0906-14.2102-25.319215.8408
102.90681.12840.21324.05870.02091.3721-0.07160.05930.16890.11410.04270.1205-0.1945-0.21250.03540.07170.0321-0.02690.12770.0030.050721.9487-10.704261.1953
110.5294-0.22750.42951.9782-0.03211.075-0.1074-0.03640.1314-0.0244-0.06010.0018-0.17250.07640.1410.09660.01-0.02050.0575-0.01780.111131.4902-13.826957.2025
120.1897-0.0752-0.13990.21510.13380.2237-0.02770.0194-0.0543-0.01450.0187-0.02010.0492-0.01310.03530.0963-0.0229-0.03510.0178-0.00260.08933.456-26.169234.1508
130.8420.0523-0.4560.7702-0.1070.616-0.02510.1177-0.0245-0.07220.01040.15790.1529-0.1403-0.00410.0772-0.0186-0.02490.03520.00810.117623.7507-29.565333.1231
141.33391.13840.87620.97950.66271.4307-0.06270.1286-0.1767-0.05330.1029-0.08510.08310.1548-0.04260.0613-0.00930.00240.0382-0.00910.121736.3891-28.856647.5916
150.81440.0491-0.02361.1574-0.18810.6215-0.0227-0.0555-0.0770.06670.037-0.08380.01710.0078-0.00420.11560.004-0.0070.02270.00580.077230.8495-23.56252.116
160.13940.0782-0.02870.1774-0.09060.2430.02720.01120.0938-0.01560.0028-0.0621-0.0935-0.010.00930.08870.0058-0.0192-0.02190.02110.136627.1617-11.437239.2945
170.6225-0.09220.2130.6573-0.46240.89720.026-0.023-0.02770.112-0.04130.13940.07150.00670.00340.09160.0097-0.00110.02860.00540.091822.0417-17.362848.0557
180.24160.2342-0.171.2694-0.31260.72380.03310.01230.12690.05690.05370.0771-0.1132-0.0136-0.10740.10590.0054-0.02430.0267-0.00110.136423.1756-12.25251.323
191.39480.7791-0.67114.8512-0.31811.5033-0.1342-0.11440.2146-0.05020.10680.4492-0.2029-0.14960.02770.110.045-0.04760.1186-0.02110.09816.4372-9.25953.8869
200.3466-0.0514-0.20480.1807-0.04330.69920.0116-0.03160.0263-0.00160.01790.0048-0.0829-0.0623-0.0090.0808-0.0034-0.03580.0153-0.00790.1114.111124.562327.3487
213.05510.5032-1.36581.0885-0.82522.78190.042-0.104-0.376-0.0006-0.04760.26460.3107-0.25650.03180.0986-0.0686-0.03480.17-0.00110.19374.739610.52118.6893
220.09920.02620.08360.30970.05620.36060.0188-0.0023-0.02020.03350.07080.03250.0686-0.0269-0.04990.0775-0.0021-0.0190.02020.00360.119715.583113.32322.6883
230.4983-0.0298-0.10690.464-0.03250.44430.0005-0.07950.0827-0.02950.01780.019-0.0945-0.0367-0.03050.08050.0043-0.03120.0278-0.01070.10339.713229.322925.2361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 68 )A26 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 118 )A69 - 118
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 179 )A119 - 179
4X-RAY DIFFRACTION4chain 'A' and (resid 180 through 290 )A180 - 290
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 68 )B26 - 68
6X-RAY DIFFRACTION6chain 'B' and (resid 69 through 118 )B69 - 118
7X-RAY DIFFRACTION7chain 'B' and (resid 119 through 179 )B119 - 179
8X-RAY DIFFRACTION8chain 'B' and (resid 180 through 271 )B180 - 271
9X-RAY DIFFRACTION9chain 'B' and (resid 272 through 290 )B272 - 290
10X-RAY DIFFRACTION10chain 'C' and (resid 26 through 50 )C26 - 50
11X-RAY DIFFRACTION11chain 'C' and (resid 51 through 68 )C51 - 68
12X-RAY DIFFRACTION12chain 'C' and (resid 69 through 98 )C69 - 98
13X-RAY DIFFRACTION13chain 'C' and (resid 99 through 142 )C99 - 142
14X-RAY DIFFRACTION14chain 'C' and (resid 143 through 167 )C143 - 167
15X-RAY DIFFRACTION15chain 'C' and (resid 168 through 195 )C168 - 195
16X-RAY DIFFRACTION16chain 'C' and (resid 196 through 229 )C196 - 229
17X-RAY DIFFRACTION17chain 'C' and (resid 230 through 251 )C230 - 251
18X-RAY DIFFRACTION18chain 'C' and (resid 252 through 271 )C252 - 271
19X-RAY DIFFRACTION19chain 'C' and (resid 272 through 290 )C272 - 290
20X-RAY DIFFRACTION20chain 'D' and (resid 26 through 98 )D26 - 98
21X-RAY DIFFRACTION21chain 'D' and (resid 99 through 118 )D99 - 118
22X-RAY DIFFRACTION22chain 'D' and (resid 119 through 179 )D119 - 179
23X-RAY DIFFRACTION23chain 'D' and (resid 180 through 290 )D180 - 290

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