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- PDB-5f83: Imipenem complex of the GES-5 C69G mutant -

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Open data


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Basic information

Entry
Database: PDB / ID: 5f83
TitleImipenem complex of the GES-5 C69G mutant
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / antibiotic resistance / hydrolase / carbapenemase / imipenem / mutant / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IM2 / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI089726 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Role of the Conserved Disulfide Bridge in Class A Carbapenemases.
Authors: Smith, C.A. / Nossoni, Z. / Toth, M. / Stewart, N.K. / Frase, H. / Vakulenko, S.B.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)58,7284
Polymers58,1262
Non-polymers6032
Water7,044391
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3642
Polymers29,0631
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3642
Polymers29,0631
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.920, 81.483, 71.716
Angle α, β, γ (deg.)90.000, 101.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase / / GES-5


Mass: 29062.855 Da / Num. of mol.: 2 / Mutation: C69G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaGES-5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0Z8S4, 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-carboxylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form / Imipenem


Mass: 301.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M D,L-malic acid, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.38→37.3 Å / Num. all: 103863 / Num. obs: 99237 / % possible obs: 97.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.1
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.3 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Blu-Ice5data collection
XDSdata scaling
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→35.801 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 14.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.171 4832 5.01 %RANDOM
Rwork0.1396 91668 --
obs0.1412 96500 97.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.24 Å2 / Biso mean: 15.8784 Å2 / Biso min: 6.58 Å2
Refinement stepCycle: final / Resolution: 1.38→35.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 40 391 4494
Biso mean--30.86 25.15 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064187
X-RAY DIFFRACTIONf_angle_d0.955668
X-RAY DIFFRACTIONf_chiral_restr0.082654
X-RAY DIFFRACTIONf_plane_restr0.006737
X-RAY DIFFRACTIONf_dihedral_angle_d20.0321562
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.38-1.39570.21771560.15892655281185
1.3957-1.41210.21391850.1572912309795
1.4121-1.42930.23131650.14583132329799
1.4293-1.44740.18241470.13583052319999
1.4474-1.46650.19351420.13143097323998
1.4665-1.48660.16531780.12973072325098
1.4866-1.50780.18781550.11943067322298
1.5078-1.53030.15551580.11573048320698
1.5303-1.55420.15091620.11243013317597
1.5542-1.57970.17311490.11563009315895
1.5797-1.60690.18131720.11023045321798
1.6069-1.63610.13891490.1123112326199
1.6361-1.66760.15331830.11183105328899
1.6676-1.70170.15971500.11973079322999
1.7017-1.73870.17341610.12383077323898
1.7387-1.77910.15231530.12573093324698
1.7791-1.82360.20511520.12723024317698
1.8236-1.87290.16681570.12763032318996
1.8729-1.9280.15151680.13033054322298
1.928-1.99020.15171720.13363099327199
1.9902-2.06140.16821880.13233078326699
2.0614-2.14390.15581460.13223140328698
2.1439-2.24140.16221660.13123045321198
2.2414-2.35960.17321520.14073044319697
2.3596-2.50740.17641410.15223088322998
2.5074-2.70090.20031660.1553117328399
2.7009-2.97260.16461570.16133099325699
2.9726-3.40250.18151710.16123078324997
3.4025-4.28560.16221620.14353085324797
4.2856-35.81290.17231690.14943117328697

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