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- PDB-5dva: Fragments bound to the OXA-48 beta-lactamase: Compound 1 -

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Basic information

Entry
Database: PDB / ID: 5dva
TitleFragments bound to the OXA-48 beta-lactamase: Compound 1
ComponentsBeta-lactamase
KeywordsHYDROLASE / inhibitor / complex / fragment / lactamase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(pyridin-4-yl)benzoic acid / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.50003891197 Å
AuthorsLund, B.A. / Christopeit, T. / Leiros, H.-K.S.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Screening and Design of Inhibitor Scaffolds for the Antibiotic Resistance Oxacillinase-48 (OXA-48) through Surface Plasmon Resonance Screening.
Authors: Lund, B.A. / Christopeit, T. / Guttormsen, Y. / Bayer, A. / Leiros, H.K.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,06010
Polymers113,1924
Non-polymers8686
Water11,512639
1
A: Beta-lactamase
hetero molecules

C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0305
Polymers56,5962
Non-polymers4343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y+1/2,-z+1/21
2
D: Beta-lactamase
hetero molecules

B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0305
Polymers56,5962
Non-polymers4343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_795-x+5/2,-y+4,z+1/21
3
B: Beta-lactamase
hetero molecules

D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0305
Polymers56,5962
Non-polymers4343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_794-x+5/2,-y+4,z-1/21
4
C: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0305
Polymers56,5962
Non-polymers4343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_745-x+2,y-1/2,-z+1/21
Buried area2000 Å2
ΔGint-9 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.037, 109.660, 124.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Beta-lactamase


Mass: 28298.029 Da / Num. of mol.: 4 / Fragment: UNP Residues 22-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical
ChemComp-5FL / 3-(pyridin-4-yl)benzoic acid


Mass: 199.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H9NO2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5 8-12% PEG8000 4% 1-butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.5→19.5 Å / Num. obs: 43599 / % possible obs: 99 % / Redundancy: 2 % / Biso Wilson estimate: 28.2501862195 Å2 / Net I/σ(I): 4
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2995 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_2328refinement
XDS20141118data reduction
PHASER2.5.6phasing
Aimless0.5.23data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.50003891197→19.9456465678 Å / SU ML: 0.322668444729 / Cross valid method: FREE R-VALUE / σ(F): 1.33346939847 / Phase error: 34.785499436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.286625681077 3992 4.85757048466 %
Rwork0.231534375454 78189 -
obs0.234174451067 43599 99.0597991827 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.2515689691 Å2
Refinement stepCycle: LAST / Resolution: 2.50003891197→19.9456465678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7928 0 62 639 8629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002121634648138229
X-RAY DIFFRACTIONf_angle_d0.45347184280911135
X-RAY DIFFRACTIONf_chiral_restr0.04220218258061157
X-RAY DIFFRACTIONf_plane_restr0.001578765356921520
X-RAY DIFFRACTIONf_dihedral_angle_d17.61259010594867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52940.3499836934911420.3096467203272713X-RAY DIFFRACTION99.2353145638
2.5294-2.56020.3322291930951450.3048932514482696X-RAY DIFFRACTION99.370409234
2.5602-2.59250.3193249453081390.3098170456962733X-RAY DIFFRACTION99.0344827586
2.5925-2.62660.4070091474661050.3044870044192672X-RAY DIFFRACTION98.440269408
2.6266-2.66250.3804985274221280.3066460212212673X-RAY DIFFRACTION98.4188334505
2.6625-2.70040.4033359782061190.3147430187922749X-RAY DIFFRACTION98.998964446
2.7004-2.74060.385162747321280.2816620131242669X-RAY DIFFRACTION99.2547906317
2.7406-2.78330.3111484466391250.2877621178412695X-RAY DIFFRACTION99.1212653779
2.7833-2.82880.3426668430041300.2723747481282727X-RAY DIFFRACTION99.0981616372
2.8288-2.87750.3059027459851430.2831481727312677X-RAY DIFFRACTION99.2608236536
2.8775-2.92960.3425484578271480.2833823901732705X-RAY DIFFRACTION99.3038635573
2.9296-2.98580.3099341578451610.2841785681412638X-RAY DIFFRACTION98.9395546129
2.9858-3.04650.3076920191181370.2711968925642775X-RAY DIFFRACTION98.9802855201
3.0465-3.11250.352195097561540.2705379464412647X-RAY DIFFRACTION98.8355681016
3.1125-3.18470.3450283852961410.2647949778842675X-RAY DIFFRACTION98.6339754816
3.1847-3.2640.3209619718471090.2692309407352720X-RAY DIFFRACTION99.3328651685
3.264-3.35180.3480628764861480.249727508152705X-RAY DIFFRACTION99.3384401114
3.3518-3.450.286331645391590.2267824602382674X-RAY DIFFRACTION99.4035087719
3.45-3.56070.3038747950841210.2254776738512736X-RAY DIFFRACTION99.4430908458
3.5607-3.68720.2990255234671300.2190403070742672X-RAY DIFFRACTION99.2209631728
3.6872-3.83390.2276771119261370.2086544798112744X-RAY DIFFRACTION99.6196403873
3.8339-4.0070.2070217782261340.1943900648042724X-RAY DIFFRACTION99.6860830136
4.007-4.21640.2579397827961330.192072515472682X-RAY DIFFRACTION98.5989492119
4.2164-4.47780.2040954850541390.1846413888292705X-RAY DIFFRACTION99.0250696379
4.4778-4.8190.2546169339941480.1698644352392697X-RAY DIFFRACTION99.4755244755
4.819-5.29570.2415579592161600.1762881986692665X-RAY DIFFRACTION99.0880392845
5.2957-6.04330.2421105175061380.1956150940992666X-RAY DIFFRACTION98.3859649123
6.0433-7.54470.2904224273071530.2113988518262701X-RAY DIFFRACTION98.9941033646
7.5447-19.94630.2209242874651380.17263973292654X-RAY DIFFRACTION98.2061202955
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)
10.5709905940760.0230121660448-0.1794825431291.09581242733-0.0983815766331.580579031460.0546155484111-0.074701278580.005216262497810.101480798256-0.02551703298750.0428694692083-0.01054741634080.0430043446286-0.04961742730830.451784971626-0.0103514775666-0.08273238895140.228603061694-0.02312569752560.19846885812791.0874263572263.9386729752.80163374888
20.689710029846-0.008361540913950.1745419783661.251498783910.3746251451661.347246937630.00486659821191-0.119466108878-0.04360637658230.09964049080160.03160965626050.01845743016480.0266420476779-0.0757438983507-0.03723671820440.614489282925-0.0275895436977-0.08589018115660.2560721061620.003064391642010.24032139945991.1926186564224.316111409-2.82516625874
30.573700541109-0.129015494040.2479689405381.52532059513-0.5766939882411.87397256849-0.05400721955260.004151782609870.00596645900595-0.0614137893930.1154165792970.106755984706-0.227085395739-0.0338240757793-0.06611620459790.4785898895360.0255492998729-0.0520127436890.2341925121830.007711218687420.20821646133987.3007233131226.18042152131.813898077
41.053800037990.10129891860.1628116677181.23824828446-0.1828363729731.41579404265-0.04312203893860.04267099614520.02902174188750.01819055414160.06954403446760.0653834609818-0.182892634038-0.1123225454860.004893266522060.6008787156140.01553634981760.09561867562090.2410835046580.01052353360980.238084589631132.712479826231.41022627631.7170477041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 24 through 265)
2X-RAY DIFFRACTION2(chain 'B' and resid 24 through 265)
3X-RAY DIFFRACTION3(chain 'C' and resid 24 through 265)
4X-RAY DIFFRACTION4(chain 'D' and resid 24 through 265)

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