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- PDB-5l2f: High Resolution Structure of Acinetobacter baumannii beta-lactama... -

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Basic information

Entry
Database: PDB / ID: 5l2f
TitleHigh Resolution Structure of Acinetobacter baumannii beta-lactamase OXA-51 I129L/K83D bound to doripenem
ComponentsBeta-lactamase
Keywordshydrolase/antibiotic / hydrolase / antibiotic / beta-lactamase / hydrolase-antibiotic complex
Function / homology
Function and homology information


penicillin binding / cell wall organization
Similarity search - Function
Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / 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
Chem-4J6 / ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsJune, C.M. / Powers, R.A. / Leonard, D.A. / Muckenthaler, T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R15AI082416 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI094489 United States
CitationJournal: Protein Sci. / Year: 2016
Title: The structure of a doripenem-bound OXA-51 class D beta-lactamase variant with enhanced carbapenemase activity.
Authors: June, C.M. / Muckenthaler, T.J. / Schroder, E.C. / Klamer, Z.L. / Wawrzak, Z. / Powers, R.A. / Szarecka, A. / Leonard, D.A.
History
DepositionAug 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Refinement description
Category: citation / pdbx_audit_support / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)114,85617
Polymers112,4364
Non-polymers2,42013
Water15,691871
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6834
Polymers28,1091
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6243
Polymers28,1091
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7755
Polymers28,1091
Non-polymers6664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7755
Polymers28,1091
Non-polymers6664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.367, 92.149, 170.355
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUILEILEAA36 - 27312 - 249
21GLUGLUILEILEBB36 - 27312 - 249
12GLUGLUILEILEAA36 - 27312 - 249
22GLUGLUILEILECC36 - 27312 - 249
13GLUGLULEULEUAA36 - 27412 - 250
23GLUGLULEULEUDD36 - 27412 - 250
14ASPASPLEULEUBB35 - 27411 - 250
24ASPASPLEULEUCC35 - 27411 - 250
15GLUGLUILEILEBB36 - 27312 - 249
25GLUGLUILEILEDD36 - 27312 - 249
16GLUGLUILEILECC36 - 27312 - 249
26GLUGLUILEILEDD36 - 27312 - 249

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Beta-lactamase / Beta-lactamase OXA-51 / Class D beta-lactamase


Mass: 28108.957 Da / Num. of mol.: 4 / Mutation: K83D, I129L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: oxa-51, blaOXA-51, AQ480_08190 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5QT35
#2: Chemical
ChemComp-4J6 / (4R,5S)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-3-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-4,5-dihydro-1H-pyrrole-2-carboxylic acid / Doripenem(open form, pyrroline tautomer form 1, SP2 connection to Thio)


Mass: 422.520 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H26N4O6S2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 871 / 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.17M NH4SO4, 0.085M Na cacodylate trihydrate pH6.5, 25.5% PEG 8000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.77→30 Å / Num. obs: 136010 / % possible obs: 99.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.6
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.764 / CC1/2: 0.634 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZX

4dzx
PDB Unreleased entry


Resolution: 1.77→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.162 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.089 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19174 6865 5.1 %RANDOM
Rwork0.17462 ---
obs0.17549 129053 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.694 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.98 Å2
Refinement stepCycle: 1 / Resolution: 1.77→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7495 0 151 871 8517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.027935
X-RAY DIFFRACTIONr_bond_other_d0.0010.027534
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.96510788
X-RAY DIFFRACTIONr_angle_other_deg0.622317335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9655984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99625.486350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.162151340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5221527
X-RAY DIFFRACTIONr_chiral_restr0.0710.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028999
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021784
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0482.3013888
X-RAY DIFFRACTIONr_mcbond_other2.0352.2993886
X-RAY DIFFRACTIONr_mcangle_it2.8833.444868
X-RAY DIFFRACTIONr_mcangle_other2.8833.444869
X-RAY DIFFRACTIONr_scbond_it2.9572.6734047
X-RAY DIFFRACTIONr_scbond_other2.9572.6734047
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5753.8735915
X-RAY DIFFRACTIONr_long_range_B_refined6.21528.6649362
X-RAY DIFFRACTIONr_long_range_B_other6.21528.6699363
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A160980.06
12B160980.06
21A159740.07
22C159740.07
31A163600.05
32D163600.05
41B162240.04
42C162240.04
51B159480.06
52D159480.06
61C158760.05
62D158760.05
LS refinement shellResolution: 1.766→1.812 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 481 -
Rwork0.286 9055 -
obs--95.32 %

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