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- PDB-9s5l: ADC-30 class C beta-lactamase in complex with benzoxaborole AK-412 -

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Basic information

Entry
Database: PDB / ID: 9s5l
TitleADC-30 class C beta-lactamase in complex with benzoxaborole AK-412
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / complex / boronate / covalent / antibiotic resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101021207European Union
CitationJournal: To Be Published
Title: ADC-30 class C beta-lactamase in complex with benzoxaborole AK-412
Authors: Hinchliffe, P. / Spencer, J.
History
DepositionJul 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,9318
Polymers81,1382
Non-polymers7926
Water13,547752
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9654
Polymers40,5691
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9654
Polymers40,5691
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.560, 176.460, 49.440
Angle α, β, γ (deg.)90.000, 111.990, 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: 40569.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ampC, adc30, FPK63_09015, FPK87_18695, FQZ18_06125 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: A7XM81, beta-lactamase
#2: Chemical ChemComp-XQN / 4-chloranyl-N-[[(3S)-1-oxidanyl-3H-2,1$l^{4}-benzoxaborol-3-yl]methyl]benzenesulfonamide


Mass: 337.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13BClNO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: cocrsytallisation: ADC-30 (5 mg/mL), 0.1M bis tris pH 6.5, 25% PEG3350, 2 mM AK-412

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7289 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7289 Å / Relative weight: 1
ReflectionResolution: 1.6→42.25 Å / Num. obs: 94291 / % possible obs: 99.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.069 / Net I/σ(I): 6.9
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4747 / CC1/2: 0.309 / Rpim(I) all: 0.815

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.25 Å / SU ML: 0.2347 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2024 4695 4.99 %
Rwork0.169 89487 -
obs0.1707 94182 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.47 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5689 0 48 752 6489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00625984
X-RAY DIFFRACTIONf_angle_d0.79598134
X-RAY DIFFRACTIONf_chiral_restr0.0524880
X-RAY DIFFRACTIONf_plane_restr0.00611067
X-RAY DIFFRACTIONf_dihedral_angle_d13.20312294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.38321460.37073003X-RAY DIFFRACTION99.21
1.62-1.640.41591780.35082939X-RAY DIFFRACTION99.78
1.64-1.660.34591720.32912992X-RAY DIFFRACTION99.75
1.66-1.680.31811760.3092982X-RAY DIFFRACTION99.91
1.68-1.70.31181550.2872995X-RAY DIFFRACTION99.97
1.7-1.720.31581380.28483013X-RAY DIFFRACTION99.97
1.72-1.750.32081580.27043029X-RAY DIFFRACTION99.94
1.75-1.770.31171270.24863026X-RAY DIFFRACTION99.94
1.77-1.80.25131590.23982937X-RAY DIFFRACTION99.97
1.8-1.830.27441430.23863105X-RAY DIFFRACTION100
1.83-1.860.28491520.24032911X-RAY DIFFRACTION99.97
1.86-1.90.28591440.23423094X-RAY DIFFRACTION99.91
1.9-1.930.26481430.24272915X-RAY DIFFRACTION99.77
1.93-1.970.24331500.20363090X-RAY DIFFRACTION99.72
1.97-2.020.20431680.18912894X-RAY DIFFRACTION99.51
2.02-2.060.23491440.17863065X-RAY DIFFRACTION99.6
2.06-2.110.21681570.16822930X-RAY DIFFRACTION99.26
2.11-2.170.20721690.16513003X-RAY DIFFRACTION99.37
2.17-2.240.21571570.15992956X-RAY DIFFRACTION99.05
2.24-2.310.2251630.16462980X-RAY DIFFRACTION99.05
2.31-2.390.20831450.16742972X-RAY DIFFRACTION98.55
2.39-2.490.20371710.1652926X-RAY DIFFRACTION98.19
2.49-2.60.20651620.15772893X-RAY DIFFRACTION96.98
2.6-2.740.20041400.16762819X-RAY DIFFRACTION93.49
2.74-2.910.1881510.15682948X-RAY DIFFRACTION97.88
2.91-3.130.18021620.15253009X-RAY DIFFRACTION100
3.13-3.450.20111670.14543006X-RAY DIFFRACTION99.97
3.45-3.940.14631810.12982992X-RAY DIFFRACTION100
3.95-4.970.13291710.11643018X-RAY DIFFRACTION100
4.97-42.250.16981460.14143045X-RAY DIFFRACTION99.63
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)
11.65121185870.649117336310.2083270327091.140270101360.5555277806261.409438119270.028275941339-0.171507650310.3308933729940.0713958169079-0.05377693823740.175147238004-0.152534305755-0.08630686377460.01308769637040.1326650075580.008918840583940.005919382774580.141267015609-0.005999575375580.20430458941421.923076531232.334660507712.6099745058
22.01189725416-0.245479120786-0.689506819851.699407490760.1799510742962.42528261369-0.1246589638080.304456940362-0.147340354251-0.1333941202050.03702539600340.1019504643190.281011335642-0.156464785630.08392253756920.201511539801-0.0360642562917-0.006120519951980.191209196226-0.0251727551880.13653486046719.62862609627.77295178785-8.90647760599
32.438250346320.3787485649660.2003697536510.641977115330.172364334731.103350954390.004173570167040.1697448303560.229011256389-0.09575260869270.03132186851780.0859684037863-0.0892938245322-0.0486185517135-0.03876984878230.1498064482820.00266606740031-0.01312305768930.1406997573110.04034123715210.17799149255120.132087580328.5334637464-1.43031271558
41.64541465674-0.676170036041-0.09874368797032.792130764020.1340214154693.15176141152-0.0562399406753-0.052211152925-0.1638939261640.0505266261424-0.02591029416980.1707666602310.325763039851-0.18215439726-0.008513720621260.143900184159-0.03277416240120.02285667537930.1537363051640.01705296026060.16334147776511.436244902610.470511720811.313128531
51.464367923110.626223657984-0.1097357840281.31279721070.1205924548231.26764189131-0.00542934354133-0.1270347708970.04787216094880.15831848799-0.01418573185160.0368517011670.0249569223637-0.02458160739730.03436839457520.145407630791-0.000957809796264-0.003618062385540.1749294918060.006197437760150.15650310418117.947863952323.89901954714.8480320907
60.891094686278-0.967026816881-0.03843680816433.19786145133-1.836638194851.82935300745-0.124615445956-0.241356738391-0.0118006929560.69581813399-0.0485158568231-0.358035764383-0.3241217534440.1909393685650.0650343510710.268918834842-0.0172770819329-0.0812956546080.203396212445-0.002416434660080.18064560896136.9308759923-33.56456089932.3542718581
72.43379360207-0.341092704375-0.05344402794613.24885095589-1.353579055382.733875962510.1196245330630.1768210016570.138393314765-0.257307381761-0.0607925368862-0.0899309738344-0.1262642904280.00469632290835-0.06797093498580.24564684970.01196069349520.02779421536240.141746097750.0004948765016640.14438230537728.5077232671-13.30748319868.1525152892
80.707625290911-0.5446957347830.01963531753783.94618288404-1.632144650042.324567453220.0364204055084-0.01958235835910.0499492582274-0.154667994505-0.266156971563-0.5709126682960.04623236483260.3349752944330.1647394002430.1400726192970.0005778730937020.006200993976150.2120945096710.0202620522170.24359928962340.6779282665-29.790312582818.7509831671
91.7678020685-0.7322202017480.09007583944742.88084252799-1.369454209792.28900512523-0.111781644866-0.1979514164310.3045204461280.8150689976110.117050024306-0.101277178394-0.709037783931-0.006720410232860.03387637625050.4985218534330.0157975416543-0.01234379026330.192532502294-0.0486957769480.20381166358728.1787568585-13.623318388629.0752313513
101.97387517744-0.776188363683-0.03562291719273.37230557014-0.2104908132092.12447548572-0.111583356881-0.2867364915780.1212940642060.6417041349060.06339317204230.0836154459515-0.452565161687-0.05260486281940.0953646171860.3107086226740.0134798613311-0.0006632918094160.167743660056-0.005412156443550.15428503771929.6626942765-27.43585688932.3800139205
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 79 )BA1 - 791 - 79
22chain 'B' and (resid 80 through 166 )BA80 - 16680 - 166
33chain 'B' and (resid 167 through 256 )BA167 - 256167 - 256
44chain 'B' and (resid 257 through 307 )BA257 - 307257 - 307
55chain 'B' and (resid 308 through 359 )BA308 - 359308 - 359
66chain 'A' and (resid 1 through 79 )AC1 - 791 - 79
77chain 'A' and (resid 80 through 166 )AC80 - 16680 - 166
88chain 'A' and (resid 167 through 239 )AC167 - 239167 - 239
99chain 'A' and (resid 240 through 307 )AC240 - 307240 - 307
1010chain 'A' and (resid 308 through 357 )AC308 - 357308 - 357

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