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- PDB-6skp: OXA-10_IPM. Structural insight to the enhanced carbapenem efficie... -

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Basic information

Entry
Database: PDB / ID: 6skp
TitleOXA-10_IPM. Structural insight to the enhanced carbapenem efficiency of OXA-655 compared to OXA-10.
ComponentsBeta-lactamase
KeywordsANTIBIOTIC / Class D beta-lactamase / crystal structures / Carbapenemases / Antibiotic resistance
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding / 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
Chem-IM2 / TRIETHYLENE GLYCOL / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.891 Å
AuthorsLeiros, H.-K.S.
CitationJournal: Febs Open Bio / Year: 2020
Title: Structural insights into the enhanced carbapenemase efficiency of OXA-655 compared to OXA-10.
Authors: Leiros, H.S. / Thomassen, A.M. / Samuelsen, O. / Flach, C.F. / Kotsakis, S.D. / Larsson, D.G.J.
History
DepositionAug 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _citation.country / _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 / _citation_author.identifier_ORCID / _citation_author.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9396
Polymers59,1632
Non-polymers7764
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-26 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.933, 124.794, 48.480
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: 29581.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Lysie 70 is carboxulated / Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaoxa-10, blaOXA-10, oxa-10, BK373_28375, CQP61_30695, E4Z89_25540, FORC82_p097
Production host: Escherichia coli (E. coli) / References: UniProt: Q7BNC2, beta-lactamase
#2: Chemical ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 11.8 mg/ml 20-23% PEG 3350 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.891→45.19 Å / Num. obs: 580336 / % possible obs: 99.03 % / Redundancy: 4.8 % / Biso Wilson estimate: 28.58 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1675 / Net I/σ(I): 12.33
Reflection shellResolution: 1.891→1.96 Å / Rmerge(I) obs: 1.731 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 51160 / CC1/2: 0.553 / % possible all: 92.44

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4s2o

4s2o


Resolution: 1.891→45 Å / SU ML: 0.2452 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7377
RfactorNum. reflection% reflection
Rfree0.2476 2098 4.52 %
Rwork0.2161 --
obs0.2175 46464 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.36 Å2
Refinement stepCycle: LAST / Resolution: 1.891→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 51 317 4250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134090
X-RAY DIFFRACTIONf_angle_d1.32425532
X-RAY DIFFRACTIONf_chiral_restr0.0601604
X-RAY DIFFRACTIONf_plane_restr0.0089716
X-RAY DIFFRACTIONf_dihedral_angle_d4.33323362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.891-1.940.37331240.33782633X-RAY DIFFRACTION88.79
1.94-1.980.30571380.27872916X-RAY DIFFRACTION99.97
1.98-2.040.29781390.25312932X-RAY DIFFRACTION99.48
2.04-2.10.25481390.24062957X-RAY DIFFRACTION100
2.1-2.160.26921380.2282923X-RAY DIFFRACTION100
2.16-2.240.2551400.22692940X-RAY DIFFRACTION99.97
2.24-2.330.24391400.21682970X-RAY DIFFRACTION99.97
2.33-2.440.26281400.21782964X-RAY DIFFRACTION99.94
2.44-2.570.22951410.20772979X-RAY DIFFRACTION99.97
2.57-2.730.2451400.20412969X-RAY DIFFRACTION99.97
2.73-2.940.2571400.21212970X-RAY DIFFRACTION100
2.94-3.230.22611430.20243009X-RAY DIFFRACTION99.68
3.23-3.70.23561420.20383014X-RAY DIFFRACTION99.94
3.7-4.660.20781440.19323039X-RAY DIFFRACTION99.69
4.66-450.27521500.22973151X-RAY DIFFRACTION98.27
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)
12.309966212230.528041015376-3.124044633430.8670862994470.2703999737346.1878137258-0.554750602024-0.935802129688-0.4371325280660.5089034653580.142216118223-0.407872741230.4772546693781.245554745530.2859885658720.4954162639360.188751856467-0.09025891720020.541836326370.04733617014390.4441760443664.52841308973-15.57808336671.0351504248
22.27610281856-1.199009931930.6323681046453.47169360657-1.268664956131.90916011696-0.01298038105380.0117568842809-0.032428001312-0.09360963913020.0353015204511-0.2690207805160.2629048841440.254449855742-0.005151556542590.2129306330240.0338408844908-0.006172315812480.167882501122-0.04244482009860.193638554707-5.06594098603-7.7045458881461.2105484757
32.115381481110.322062527425-3.269843011913.282511988771.213737145573.028850121220.1850778310130.06795274249970.327733723157-0.167036853150.07308565114550.279611228325-0.592308504441-0.00977321739574-0.3013354521520.2444357666540.00614936358442-0.03378094612070.2426082897040.03372417886370.245479787324-18.699971920314.558552337460.9961843851
48.86150160093-0.0855140265884-4.320062874718.84080065189-3.471283715783.602534083150.169765887047-0.6090457285170.4226592962480.496419945344-0.145579998837-0.052253053199-0.284079623450.3970769634110.01127280519710.230992179883-0.0362081999162-0.03157105190810.171932010009-0.02596020487480.176342552456-14.070294459811.612922030268.0497124565
51.721412745230.227368065573-0.005843670098171.951216935020.09912130396531.3107786410.02597841221590.0880428928828-0.0733776909082-0.1620885714730.00705992263027-0.08926396414450.07752556137860.11651960469-0.02574624577020.2411935300170.0221042533362-0.002604845307870.192325467557-0.002034184738640.170867341953-10.74206053480.28923149706956.5604476671
68.113210947143.42673532114-5.371209488032.50734729545-1.95568139346.87902797347-0.184782437493-0.230666349613-0.2735816030750.0123594169648-0.0236782932531-0.2428219940150.5195929447640.001241534593280.178694303770.3250510716480.07714341491-0.03303059883730.187362193089-0.01495436891080.210465995121-9.60099334354-7.3350383229969.6612736939
76.771428250043.44608321964-3.481793928914.73449277254-3.84791622423.278060138710.218640785159-0.76116574869-0.342789568487-0.0241543733508-0.448551235456-0.355189330138-0.06531705828370.9507953363490.195092493560.317377186970.0528999121575-0.0403281954990.307888691921-0.0353183290860.2017158852790.129548661123-5.4978183749666.5399193534
82.12284087082.67961064902-4.42558705843.45702284845-1.369145057546.508652261580.491396394249-0.746374701687-0.2717429914790.352214734798-0.38959041059-0.329743995668-0.3306840728380.896263408828-0.08910914659110.3616369495850.018596211579-0.08466224274960.489890564976-0.02028822717090.2888234384331.88538330523-4.043214404173.9100849348
92.29873548412-7.586898336215.509050812888.71709453789-6.327892916464.81690743973-0.336297794466-1.270707493860.1055495862391.096449107660.6996764456150.127989976060.114200104219-0.581705105823-0.1356589080640.620961612274-0.0643526309671-0.008892517633710.665715983889-0.05658761932090.3148478854174.4229162521237.72089718774.3373335799
102.01804642244-0.717976111618-1.064679816394.09237033291.845316651323.32949857783-0.0880753243252-0.05246020412910.05963202589230.1084663481640.0985023921701-0.0807889762069-0.3181277545180.517666511434-0.0256242710320.237390916253-0.0815586932095-0.02736571641710.277259162970.04546806538850.1599785870637.642034743631.734521880960.8797579146
117.92942623967-0.1356068686582.275383085774.49508687758-1.262148142973.627331166620.1386899864170.206434506267-0.7787539570170.0334876694745-0.0662526800928-0.3015555682540.1717789312530.715903398827-0.07936989853610.284145081269-0.009463928796680.09872992297410.46538170603-0.07135121388890.46227120693718.452831200611.229944374353.8563643685
122.770165306630.2233563139030.2083318099723.28603199346-0.2415439774152.83971945161-0.03696829481130.376362166237-0.0670971443714-0.06364662906290.0424999506399-0.251556914503-0.09710834868720.454573698385-0.003022731367390.187315307857-0.04565869170130.002727808127430.31461704427-0.02569011548850.17760909091510.499631089325.764683361854.7168615743
136.30509777891.918045427022.246495269372.925179607530.6595497794913.941718094660.62195458242-1.00881465088-0.5014834566420.814633626088-0.382938526989-0.2607043622340.263014610030.0987131695428-0.2167070720980.419821040048-0.0588448970867-0.06995126231910.3655973842520.07033491427720.2514900005177.5984453999427.198400891871.3634432418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 99 )
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 116 )
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 208 )
6X-RAY DIFFRACTION6chain 'A' and (resid 209 through 228 )
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 243 )
8X-RAY DIFFRACTION8chain 'A' and (resid 244 through 265 )
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 35 )
10X-RAY DIFFRACTION10chain 'B' and (resid 36 through 79 )
11X-RAY DIFFRACTION11chain 'B' and (resid 80 through 116 )
12X-RAY DIFFRACTION12chain 'B' and (resid 117 through 228 )
13X-RAY DIFFRACTION13chain 'B' and (resid 229 through 265 )

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