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- PDB-6wgr: The crystal structure of a beta-lactamase from Staphylococcus aur... -

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Basic information

Entry
Database: PDB / ID: 6wgr
TitleThe crystal structure of a beta-lactamase from Staphylococcus aureus subsp. aureus USA300_TCH1516
ComponentsBeta-lactamase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Membrane lipoprotein, lipid attachment site / Prokaryotic membrane lipoprotein lipid attachment site / 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 ...Membrane lipoprotein, lipid attachment site / Prokaryotic membrane lipoprotein lipid attachment site / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsTan, K. / Wu, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: The crystal structure of a beta-lactamase from Staphylococcus aureus subsp. aureus USA300_TCH1516
Authors: Tan, K. / Wu, R. / Endres, M. / Joachimiak, A.
History
DepositionApr 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 / software
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
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4637
Polymers87,6563
Non-polymers8074
Water7,764431
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4572
Polymers29,2191
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)29,2191
Polymers29,2191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7874
Polymers29,2191
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.357, 52.505, 89.662
Angle α, β, γ (deg.)75.625, 81.053, 64.124
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Beta-lactamase


Mass: 29218.551 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: blaZ, SAP015A_001, SUA_0014, SUC_0012, SUD_0013p2, SUI_0012p2, SUJ_0013p2, SUK_0013p2, SUP_0013
Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)
References: UniProt: D2J684, UniProt: P00807*PLUS, beta-lactamase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES:NaOH 20% (w/v) PEG 4000, 10% (v/v) 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→43.2 Å / Num. obs: 66212 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 24.04 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.064 / Rrim(I) all: 0.136 / Χ2: 1.598 / Net I/σ(I): 16.4
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 3 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 3126 / CC1/2: 0.555 / CC star: 0.845 / Rpim(I) all: 0.511 / Rrim(I) all: 0.963 / Χ2: 0.515 / % possible all: 92.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.17.1_3660refinement
HKL-3000phasing
HKL-3000data scaling
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BLM

3blm


Resolution: 1.88→43.15 Å / SU ML: 0.2169 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.084
RfactorNum. reflection% reflection
Rfree0.2058 3208 4.85 %
Rwork0.167 --
obs0.1689 66183 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.67 Å2
Refinement stepCycle: LAST / Resolution: 1.88→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6161 0 51 431 6643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00756332
X-RAY DIFFRACTIONf_angle_d0.85528512
X-RAY DIFFRACTIONf_chiral_restr0.0542954
X-RAY DIFFRACTIONf_plane_restr0.00481076
X-RAY DIFFRACTIONf_dihedral_angle_d20.60722481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.910.31691320.27622405X-RAY DIFFRACTION86.62
1.91-1.940.29121270.24022709X-RAY DIFFRACTION95.49
1.94-1.970.26851560.21312655X-RAY DIFFRACTION97.23
1.97-2.010.2151530.20042754X-RAY DIFFRACTION98.44
2.01-2.040.2661450.18962724X-RAY DIFFRACTION99.17
2.04-2.080.24631390.18432762X-RAY DIFFRACTION98.77
2.08-2.120.23861330.18362773X-RAY DIFFRACTION98.84
2.12-2.170.25421470.18072744X-RAY DIFFRACTION98.4
2.17-2.220.2131610.17352710X-RAY DIFFRACTION98.39
2.22-2.280.24221210.17312789X-RAY DIFFRACTION98.78
2.28-2.340.25311400.172719X-RAY DIFFRACTION98.52
2.34-2.410.2071340.1692814X-RAY DIFFRACTION99.13
2.41-2.480.20451440.16412770X-RAY DIFFRACTION99.25
2.48-2.570.22681450.16552710X-RAY DIFFRACTION99.1
2.57-2.680.22861450.16852753X-RAY DIFFRACTION98.57
2.68-2.80.2271290.16862816X-RAY DIFFRACTION99.16
2.8-2.940.24491270.17812782X-RAY DIFFRACTION99.49
2.94-3.130.23951130.1812770X-RAY DIFFRACTION99.48
3.13-3.370.19041400.17322774X-RAY DIFFRACTION99.01
3.37-3.710.1861320.15982791X-RAY DIFFRACTION98.65
3.71-4.250.18021420.14132763X-RAY DIFFRACTION99.45
4.25-5.350.14871340.13032750X-RAY DIFFRACTION98.94
5.35-43.150.16771690.16112738X-RAY DIFFRACTION98.91
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)
11.476655047720.508311836108-0.8906017768632.52113123882-1.049398531962.065978849410.1351172816790.1582258066180.403991512667-0.3055685203120.03834150833630.180211243364-0.389927419583-0.476978252167-0.122048422320.2738048049750.1069005714870.01254057949360.2132251215720.03341084863290.275214659797-12.392533355113.1201389881-0.41392837619
21.11841327596-0.7117259454860.02084072845041.14647740672-0.2091415478181.040979227110.05099920197240.1153801514070.0135547994793-0.178714056195-0.02601260597780.0477597900073-0.00117498946902-0.194641081266-0.05417385571420.1837637526680.0041593402728-0.02071937768140.21453426603-0.01087083065280.179135003527-5.03918811714-1.975192375-1.60808398407
32.61803788190.159717630467-0.5129482734472.4348123393-1.211443695423.603883455560.009483523558620.0841089658195-0.158466962621-0.361962217298-0.131101833839-0.4588975409320.3117077096120.5836571111540.08968893004380.2045427094970.04225078399040.05778058371760.246206917919-0.02017458095030.29910013310516.5175348104-10.36644241670.359252464271
42.95457787846-0.86800709685-0.2071356516372.95738303375-0.2845047484562.847687981040.09827246085390.0741273028784-0.120961410277-0.16730315583-0.00121373963604-0.1444484005290.1563745517580.251527727316-0.119853085560.1596736728820.01682396169120.009291172595340.184823724896-0.01709807667120.24756599120712.090938599-8.037797690610.796589215715
52.73297693364-0.771250215705-1.536888015871.53879204217-0.6713729307653.207808434330.0838008087366-0.0139223557091-0.349240395642-0.256107002526-0.04711538435080.05391837775740.353645133875-0.135514588476-0.04541926280180.291218078541-0.0274863683398-0.06406439140620.205267705151-0.0516256434610.282995490484-3.73634071656-11.4925985236-6.36375509678
63.0860225964-0.405261351386-1.317519050652.49317306868-0.2296061060295.089787401070.1431289603410.4466868197750.0921206819102-0.351760461317-0.06712532534140.09145868938610.0821331524436-0.383012384258-0.06257265972390.2220196250280.027361901226-0.02760737341370.194135899337-0.0003028045027740.180854860488-5.12885045478-1.97099422292-7.89852215715
72.92840313677-0.570652088480.3312264067073.35455600106-1.032480833872.200900270720.0661612260863-0.2095793535840.1074064737990.203082546511-0.0714412377639-0.206744407655-0.1584518888620.0990252472432-0.02213615072430.139732851431-0.00158716864150.002847804872960.170057072771-0.03537381596620.1513125376482.098787081491.6987811224410.7651778086
82.67086509103-0.254818479654-0.3977896202412.485737762570.5492392116922.674975641640.1756365549470.04490125786730.360161206263-0.199168465401-0.0829709625843-0.093334635519-0.370053527871-0.0692778468888-0.08605787095810.1699171634910.01651861767810.01526496659180.1182992214250.006122116483740.192475052868-3.512624510629.551197117890.908506971875
94.491271404462.66398656061-1.226018299684.42723259271-1.687433619443.010527964910.1067876203750.02595191753460.535392832721-0.1453487418450.01684359799820.148329986532-0.431756166859-0.273616661413-0.08211624716740.2703814932770.1027528396250.009715078811240.228951123529-0.03253168056960.353556292517.1475181932931.528960396231.0090051985
100.784870016351-0.0531668996729-0.4399801701681.12198380672-0.02773985554141.22456499970.043558442372-0.07884489064160.07638051890250.1009928817410.000767553039155-0.0252116483488-0.08131220832020.108288665236-0.05355331955040.150436509925-0.00726285688002-0.03333685452150.182745687903-0.005296232727090.19022111013221.395100782119.223088513326.7680374088
112.52286580276-0.348539232295-2.005325005852.189485149170.01486868220254.13630383191-0.308330794034-0.133381920344-0.3345488114550.1925336367030.137788125590.08435874390040.7938855966790.04694709160720.1894313793740.2552634904180.01620272921470.004278711329880.1791097679170.03455816220560.26118679510620.7365734412-7.5652517123226.7813004689
122.00622693151-0.306627228372-0.7674408610653.424267800750.951980023622.27544191227-0.11723894492-0.124180845551-0.157802844180.2912332003320.09790678113730.0918152038610.3343354850060.136220424172-0.01117200615850.1964667900830.0356852172702-0.005415663540260.1738676399740.02365480178150.22012184796320.9325147022-2.4849152171225.9424627157
131.160479099520.0706581711401-1.408716486162.2594134555-0.1278315863963.18266828769-0.00886788283866-0.0856586750329-0.1129930772120.2709982441090.173199610181-0.2751266176680.2390916065860.536844051252-0.1648284728660.1672420759190.0488142360367-0.0767426186750.307799793964-0.05059405332790.22661955506630.8779100610.072831567433.1828786015
142.242351796050.316529900941-1.425728842392.82086068437-0.04082739019764.852392191620.0382363656008-0.136071351962-0.04113937652070.275031196631-0.0839115310315-0.02674800037380.1489119549070.3522413477660.03469917132570.1386400546010.0346917008368-0.03340844877590.188246476943-0.01682688995650.17277416173523.097861165615.542351404434.6416438167
152.15622046416-0.681448318973-0.7648790396142.311403437131.061745480061.851937410090.05563141853140.311233694586-0.0355059670929-0.158637726928-0.1046402591220.150137409603-0.00976588066286-0.1493512863910.03221984595260.1524040298560.0176356892923-0.04488988025990.1779759608510.01785373085180.17212853399116.522111497610.816877713615.9814049253
161.256718190290.0309166424080.03808196933392.15426919409-0.09685064734622.51084029370.001688042130390.008290251080070.1372647513110.00566493505024-0.01202880234260.273293894369-0.161809940561-0.131637159152-0.000950919432740.1325496520530.00901710211344-0.01363278091280.1563969173370.003084169052790.22264774735812.034128079119.289173140825.9179856461
170.9300980604320.65223965867-0.9348658962461.57085891846-0.08991007319441.398196151540.22872249518-0.461076373782-0.03991496466820.563076773431-0.199603387173-0.273517653808-0.3437859137920.593344639651-0.02839966511710.49956913743-0.188673770189-0.03393455178360.520859033211-0.0201084625030.25987617732632.697066948836.725210218762.145331436
182.502286052790.282759399284-0.08484642469012.01898282826-0.5454479345161.752034875430.09164394815660.7761362831060.669234512104-0.3132690989760.2181336661710.333913428632-0.45320748779-0.0627171364773-0.2923235673850.481987712725-0.01052720697960.02502083332650.3352342652850.0814633728630.27987912113117.938134740846.187352066137.8394328542
195.30968855985-0.3844919777630.1138980587853.43998891276-0.2315514160313.20468572680.3967261051310.6517469565870.191521866088-0.0268584128526-0.08464679029230.231967113342-0.33286907633-0.044774908267-0.3029443516820.3226196058310.03528717722020.03758442164230.2916546371430.03505573432570.22167909982518.963663404340.454826815839.4091674977
200.3047416080770.1628088170910.5495266376190.1238323393070.5282407467392.596980253420.457651652098-0.3203659616980.5436384968480.355347853758-0.1487856712060.36169540462-0.792313869217-0.0753741404211-0.2326667447550.641665175434-0.08783751156930.2103591264250.353917210593-0.04822093202480.35850145796819.318178048348.622172824154.3549146746
213.945433024570.6253040841070.05422240443572.910127392562.022264437653.954981519080.257839064938-0.3269852421040.7226955963050.1390040625480.06201073101250.0120148511849-0.3818754980160.0234552646128-0.176257653290.695641822602-0.2404727789530.1677704684670.437176643814-0.1065208223020.38223046529232.932361754653.57306164857.103279551
221.958053075820.7730227499111.474686906744.466470708251.803245405231.467774989930.36139058632-0.5569478134290.07267889413460.748555003917-0.2357456633440.279900669961-0.4334596080790.247725134492-0.06395361093610.589320885958-0.2104299904360.1079757974140.413350707503-0.05153009945890.23879538901723.969964720139.151434853162.7816725192
236.186469601970.587172890205-0.3290502333171.80995886538-0.03425123958092.41976425190.0991798858271-0.219220880388-0.5503057938580.104714227537-0.0318754184299-0.1073727119030.114482257550.207432022843-0.08346276188960.29345995306-0.0301989250576-0.009584740476530.183404022857-0.005037511318140.19056936941924.617106171329.046573021950.4899850329
242.639723008680.530697026692-0.06089672066982.13089415720.6727379749652.434525263160.465978094163-0.486556182127-0.1002741109680.334960860467-0.242264482612-0.405450574809-0.12338829180.70521565178-0.181146027830.372880436283-0.120902880205-0.03761887956790.4093028277060.003529228149260.24567160386935.406284303634.569262430556.4435361062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 105 )
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 133 )
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 158 )
6X-RAY DIFFRACTION6chain 'A' and (resid 159 through 184 )
7X-RAY DIFFRACTION7chain 'A' and (resid 185 through 219 )
8X-RAY DIFFRACTION8chain 'A' and (resid 220 through 281 )
9X-RAY DIFFRACTION9chain 'B' and (resid 22 through 34 )
10X-RAY DIFFRACTION10chain 'B' and (resid 35 through 76 )
11X-RAY DIFFRACTION11chain 'B' and (resid 77 through 105 )
12X-RAY DIFFRACTION12chain 'B' and (resid 106 through 133 )
13X-RAY DIFFRACTION13chain 'B' and (resid 134 through 158 )
14X-RAY DIFFRACTION14chain 'B' and (resid 159 through 184 )
15X-RAY DIFFRACTION15chain 'B' and (resid 185 through 219 )
16X-RAY DIFFRACTION16chain 'B' and (resid 220 through 281 )
17X-RAY DIFFRACTION17chain 'C' and (resid 22 through 76 )
18X-RAY DIFFRACTION18chain 'C' and (resid 77 through 105 )
19X-RAY DIFFRACTION19chain 'C' and (resid 106 through 120 )
20X-RAY DIFFRACTION20chain 'C' and (resid 121 through 158 )
21X-RAY DIFFRACTION21chain 'C' and (resid 159 through 170 )
22X-RAY DIFFRACTION22chain 'C' and (resid 171 through 184 )
23X-RAY DIFFRACTION23chain 'C' and (resid 185 through 220 )
24X-RAY DIFFRACTION24chain 'C' and (resid 221 through 281 )

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