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- PDB-6v7t: Crystal structure of CTX-M-14 E166A/D240G beta-lactamase in compl... -

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Basic information

Entry
Database: PDB / ID: 6v7t
TitleCrystal structure of CTX-M-14 E166A/D240G beta-lactamase in complex with ceftazidime
ComponentsBeta-lactamase
KeywordsHYDROLASE / drug resistance / protein evolution / conformational change / enzyme kinetics / enzyme catalysis / protein stability / protein-drug interaction
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic / metal ion binding
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
ACYLATED CEFTAZIDIME / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsBrown, C.A. / Hu, L. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32956 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Antagonism between substitutions in beta-lactamase explains a path not taken in the evolution of bacterial drug resistance.
Authors: Brown, C.A. / Hu, L. / Sun, Z. / Patel, M.P. / Singh, S. / Porter, J.R. / Sankaran, B. / Prasad, B.V.V. / Bowman, G.R. / Palzkill, T.
History
DepositionDec 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 3, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.4Oct 11, 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 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8504
Polymers55,9112
Non-polymers9392
Water12,701705
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4252
Polymers27,9561
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4252
Polymers27,9561
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.110, 107.330, 47.750
Angle α, β, γ (deg.)90.000, 99.860, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-lactamase


Mass: 27955.551 Da / Num. of mol.: 2 / Mutation: E166A, D240G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM465_01285, AM465_ ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM465_01285, AM465_06510, AM465_23360, APT94_14605, BEN53_26220, BET08_34355, BJJ90_27545, BK334_27290, BOH76_00730, BON63_16015, BON66_01305, BON69_22545, BON71_04040, BON75_10525, BON76_14325, BON81_01055, BON83_15455, BON86_08515, BON91_02075, BON92_04750, BON94_23850, BON95_01680, BON96_03940, BXT93_06855, C5N07_28500, C5P43_21980, CDL37_21060, CR538_26855, CRT46_23505, DW236_20870, EIA08_25160, EIA21_26975, ELT23_05930, ETN48_p0088, FNJ69_13810, FQR64_24895, FTV90_03295, pCT_085, pHK01_011, RCS103_P0010, RCS30_P0082, RCS56_P0085, RCS60_P0031, RCS63_P0006, RCS65_P0008, RCS66_P0053, SAMEA4362930_00013, SAMEA4370290_00046
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5C7, beta-lactamase
#2: Chemical ChemComp-CAZ / ACYLATED CEFTAZIDIME


Mass: 469.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H19N5O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2M Na chloride, 0.1M Tris pH 8, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999974 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999974 Å / Relative weight: 1
ReflectionResolution: 1.34→47.04 Å / Num. obs: 99523 / % possible obs: 99.44 % / Redundancy: 3.7 % / Biso Wilson estimate: 9.05 Å2 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.028 / Rrim(I) all: 0.055 / Net I/σ(I): 17.1
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.118 / Num. unique obs: 9924 / Rpim(I) all: 0.068 / Rrim(I) all: 0.137 / Χ2: 8.5 / % possible all: 99.26

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT
Resolution: 1.34→47.04 Å / SU ML: 0.0931 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.0695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1616 4992 5.02 %
Rwork0.143 94529 -
obs0.1439 99521 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.04 Å2
Refinement stepCycle: LAST / Resolution: 1.34→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 62 705 4669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00544054
X-RAY DIFFRACTIONf_angle_d0.95555534
X-RAY DIFFRACTIONf_chiral_restr0.0801655
X-RAY DIFFRACTIONf_plane_restr0.0071747
X-RAY DIFFRACTIONf_dihedral_angle_d15.7243621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.360.18771820.15893124X-RAY DIFFRACTION99.34
1.36-1.370.18561450.15763193X-RAY DIFFRACTION99.17
1.37-1.390.19621500.15013130X-RAY DIFFRACTION99.27
1.39-1.410.15641820.14673136X-RAY DIFFRACTION99.28
1.41-1.420.17191890.1393076X-RAY DIFFRACTION99.33
1.42-1.440.16641610.14113174X-RAY DIFFRACTION99.58
1.44-1.460.1691670.1383140X-RAY DIFFRACTION99.55
1.46-1.490.14861500.13543170X-RAY DIFFRACTION99.64
1.49-1.510.16331780.13873133X-RAY DIFFRACTION99.52
1.51-1.530.16812050.13573118X-RAY DIFFRACTION99.52
1.53-1.560.1351620.13473136X-RAY DIFFRACTION99.64
1.56-1.590.16391620.13093163X-RAY DIFFRACTION99.55
1.59-1.620.15971630.13513136X-RAY DIFFRACTION99.52
1.62-1.650.1511720.13673176X-RAY DIFFRACTION99.64
1.65-1.690.17931610.13753131X-RAY DIFFRACTION99.46
1.69-1.730.1951690.14233160X-RAY DIFFRACTION99.67
1.73-1.770.17161630.14513124X-RAY DIFFRACTION99.61
1.77-1.820.1591430.14643226X-RAY DIFFRACTION99.67
1.82-1.870.15491530.13853161X-RAY DIFFRACTION99.61
1.87-1.930.16521790.13893108X-RAY DIFFRACTION99.55
1.93-20.15291750.14053136X-RAY DIFFRACTION99.37
2-2.080.15431590.13633177X-RAY DIFFRACTION99.37
2.08-2.180.14191580.1373150X-RAY DIFFRACTION99.4
2.18-2.290.1591740.14333153X-RAY DIFFRACTION99.25
2.29-2.430.19021780.14853123X-RAY DIFFRACTION99.49
2.43-2.620.16141390.15273199X-RAY DIFFRACTION99.58
2.62-2.890.16521800.15623149X-RAY DIFFRACTION99.91
2.89-3.30.16871520.14953209X-RAY DIFFRACTION100
3.3-4.160.15221740.13233185X-RAY DIFFRACTION99.79
4.16-47.040.14571670.14863133X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.2218279569370.174669590653-0.07608033397920.2450132934230.0321666177990.115337204533-0.0877202631007-0.08975460184550.1941631814330.103269366846-0.05549057328580.345709790347-0.231571174655-0.178062157275-0.001160602246950.1571563605160.01873911671390.01588304586120.140213641176-0.0366613008170.159547431959-18.79549271797.065163378325.8266244956
20.1298689695920.0441706699237-0.1362080863120.4338096261260.1338489603120.2389341984150.0262802109763-0.002236763530510.104546029642-0.00535165725354-0.04561210766740.163074489878-0.100823594802-0.124806909843-0.0003958904694410.07177696268880.003501915851320.00677323455430.0859562841175-0.01520078881370.104708845978-15.46424096878.589814163613.8516959301
30.140393817955-0.0485684848902-0.1081225765830.1072789342980.008953060911010.07492539262860.01050869550970.06017295531480.0522087762943-0.02584494942540.000251762106335-0.00660436037154-0.0699375072090.00269434904954.21845970717E-50.0741905237797-0.00309054055675-0.003603430939950.07152605338510.007275285035140.0587507357134-6.82256297618-0.0265190428495-3.37368916784
40.0405494810463-0.0311072211956-0.03648866375020.082943876878-0.02663697066720.08173379733090.05304397511710.224771604402-0.00655319205275-0.130901407118-0.0359255984296-0.0579381446952-0.01477559092380.1807340212978.3416009872E-60.1145497811260.0212695115376-0.002208355746110.134279090808-0.01154390693610.0910645212012.00990360284-8.28201696525-11.2261985264
50.126323411241-0.0105293148808-0.02871529995910.04280539284280.01586310187110.07362928855210.04807178409030.0163506297992-0.1027616937570.02703752685310.00187134417275-0.04320525651520.1261881709530.1175014777470.0002463660767160.08457334801870.0151581308871-0.006427354277850.0916971877169-0.008990694269850.07920304905842.75057515493-12.163459098-0.916753968554
60.1248213587840.0772765530661-0.0456893118030.1624921041310.1309111664230.183516795125-0.01852627313440.0233132933503-0.00422286562314-0.04653806776950.04300788713060.0500328830366-0.0288358028930.022425247362-5.74780781857E-60.075647755171-0.006721688962760.0006021647496260.06793965980140.00387040316280.0692998373754-1.073777268871.11556853207-2.5438932149
70.1303537417290.0923001667142-0.09665175511010.19604129580.03166596732670.2439553331130.0124480729021-0.01714620539240.07556772362440.05297305821760.01384928379210.0170809604819-0.09973957270770.0708332725091-7.80771951635E-50.0797851081506-0.01595977241330.007688021100910.0751656513878-0.00842301886820.08334683675861.00857488878.267554078046.83079888453
80.05556139056620.01435643411440.01687568765380.06276593356670.001786589192330.1229030214940.02613988114250.0008985326682760.0409722389583-0.07566788158240.02304177962880.0462462833291-0.108854355146-0.09736951735510.004974023233550.07718799587430.003153701158550.003842764261650.08215923068580.008919881149110.0873383405984-14.22327106686.952986213454.71351168997
90.04705534364540.0176867781609-0.09965899632860.226947481868-0.06659029754660.1714809028910.04041398071450.119425084859-0.0373097715185-0.09716627552640.03869592254720.2058883391190.038961913701-0.1708367068120.0114238022120.0793396034296-0.00433494922561-0.01831271253980.09490191800940.009205691684230.0798657722059-16.447311971-4.67030358272-4.26981711792
100.109681376724-0.101476133353-0.1125214699870.09416131149210.09430887448420.370286926912-0.05154609535480.0984922374339-0.06356794515340.0694051029398-0.01258498321910.1126272601610.181590046652-0.217767252443-0.004725909750750.0898956208795-0.02662016685950.01582352377510.0899329125537-0.00374064235460.0861535398848-16.5197318206-9.3203871556814.0443004765
110.146670866429-0.138277446056-0.1495606543280.31338703313-0.03097415345180.286446276918-0.0345298554728-0.01249289292070.02110115925260.01252382112850.01363507039830.08561290284450.00618971015951-0.01372790706011.20001656089E-50.0554286767182-0.0150484137078-0.003500206524470.0624151763361-0.004251148359750.0636970954363-10.0755359801-2.6714774955311.4818652305
120.189942974425-0.0966566923624-0.2928566907540.520359294987-0.08238663833840.5144226406750.0713957687886-0.151486916184-0.1304598044530.09621924194390.03178724765890.04510764743770.0713790136741-0.09173309444340.01333704770240.0731944143114-0.0158656027894-0.002641819467950.07851444498330.002027607064340.0821564332409-11.1718120310.070402611615816.5992592292
130.256811185288-0.1536908213360.05551401194680.463655407408-0.09286344134770.261054765273-0.0116119533847-0.0631087127728-0.08864581678850.07153521728080.03711832575630.183762892920.0321630922927-0.2350984935650.01033189092990.0857174992048-0.002006468866340.01312319591380.108659230237-0.003731244520740.0674543572715-17.8451545596-1.8778550994520.8256805223
140.458413475759-0.430900128183-0.4323848186310.8859021097490.613952536610.564546862645-0.0223477040959-0.2583095272150.03991913019180.3494323393390.0756648412562-0.3107422003610.002563586085910.293071803840.02697762309710.191575809529-0.00623999321518-0.03895491046980.1385993085140.001780907194580.0970996412267-4.10909549794-26.193320117731.3341020028
150.11144469207-0.05500467498450.07851847180320.568502497145-0.1487354830180.2725698082970.04670189847480.0196133108958-0.06968434939380.0475487904781-0.0343762078899-0.05619620944330.05857955066250.1506989215290.001777313543850.08158345940210.015845567214-0.005589909668810.09197171594480.005183770354030.0788481206643-8.96512462427-33.565890874516.0645493134
160.0496020203556-0.000313576837430.05600187869920.08994351387240.007695400300730.0931677689960.1084990582060.159976966478-0.123976057409-0.184278937672-0.1279090732930.1287853287020.215204917547-0.02847367727670.0002789835547230.1668041676010.0706458300513-0.01132823475060.155163520597-0.01387528446890.140579119208-22.5252939787-31.0372040027-4.89840967022
170.48439292686-0.1651151724460.2228184532260.668382130008-0.1158978225410.7751621863860.04098273047980.0247926502333-0.0116378878759-0.0118353450127-0.03429971979770.009649743056890.008692887390220.0299375761322-0.000245496232280.059891595460.006489053413520.004316786627740.05221864106780.003525787358350.0678691336694-14.2873305186-28.513362058510.7945959617
180.2087511291260.008775394695270.3363413913720.560122872937-0.07020018987850.5364539226480.0636456931675-0.01889481192580.2704933098060.1425495597080.0157106303694-0.133851507029-0.135573326903-0.006062803876750.003920890375710.109890418864-0.003652931457230.009417931207060.07752195387690.00439033705030.103675653208-9.59895427075-23.280633271323.2607650563
190.593640238486-0.388199489519-0.4549548534011.02123415099-0.3045532730330.949793280318-0.0262991884141-0.1609515042510.162030440850.2380196782440.0164265900709-0.32397109022-0.1082435961050.366024407936-0.03206060814570.144670058505-0.0256865904401-0.02384734005150.11359924314-0.009402871916930.100749585683-3.56790102604-19.144980980825.1064674411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 128 )
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 194 )
9X-RAY DIFFRACTION9chain 'A' and (resid 195 through 213 )
10X-RAY DIFFRACTION10chain 'A' and (resid 214 through 229 )
11X-RAY DIFFRACTION11chain 'A' and (resid 230 through 251 )
12X-RAY DIFFRACTION12chain 'A' and (resid 252 through 275 )
13X-RAY DIFFRACTION13chain 'A' and (resid 276 through 290 )
14X-RAY DIFFRACTION14chain 'B' and (resid 26 through 50 )
15X-RAY DIFFRACTION15chain 'B' and (resid 51 through 85 )
16X-RAY DIFFRACTION16chain 'B' and (resid 86 through 101 )
17X-RAY DIFFRACTION17chain 'B' and (resid 102 through 251 )
18X-RAY DIFFRACTION18chain 'B' and (resid 252 through 275 )
19X-RAY DIFFRACTION19chain 'B' and (resid 276 through 290 )

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