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- PDB-4nk3: Amp-c beta-lactamase (pseudomonas aeruginosa) in complex with mk-7655 -

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Basic information

Entry
Database: PDB / ID: 4nk3
TitleAmp-c beta-lactamase (pseudomonas aeruginosa) in complex with mk-7655
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MK7 / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsScapin, G. / Lu, J. / Fitzgerald, P.M.D. / Sharma, N.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: Discovery of MK-7655, a beta-lactamase inhibitor for combination with Primaxin().
Authors: Blizzard, T.A. / Chen, H. / Kim, S. / Wu, J. / Bodner, R. / Gude, C. / Imbriglio, J. / Young, K. / Park, Y.W. / Ogawa, A. / Raghoobar, S. / Hairston, N. / Painter, R.E. / Wisniewski, D. / ...Authors: Blizzard, T.A. / Chen, H. / Kim, S. / Wu, J. / Bodner, R. / Gude, C. / Imbriglio, J. / Young, K. / Park, Y.W. / Ogawa, A. / Raghoobar, S. / Hairston, N. / Painter, R.E. / Wisniewski, D. / Scapin, G. / Fitzgerald, P. / Sharma, N. / Lu, J. / Ha, S. / Hermes, J. / Hammond, M.L.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3752
Polymers41,0241
Non-polymers3501
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.751, 72.127, 106.039
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 41024.316 Da / Num. of mol.: 1 / Fragment: Catalytic domain / Mutation: R397A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: ampC, PA4110 / Plasmid: Pet 26 / Production host: Escherichia coli (E. coli) / References: UniProt: P24735, beta-lactamase
#2: Chemical ChemComp-MK7 / (2S,5R)-1-formyl-N-(piperidin-4-yl)-5-[(sulfooxy)amino]piperidine-2-carboxamide / MK-7655, bound form


Mass: 350.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22N4O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 3350, 10% isopropanol, 100 mM Imidazole, pH=6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 9, 2007
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 27942 / Num. obs: 27131 / % possible obs: 97.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 25.4 Å2 / Rsym value: 0.121 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 10 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2742 / Rsym value: 0.457 / % possible all: 94.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.615 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21319 1356 5 %RANDOM
Rwork0.1738 ---
obs0.17582 25653 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.128 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2--0.68 Å20 Å2
3---1.09 Å2
Refine analyzeLuzzati coordinate error obs: 0.208 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 23 340 3151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222883
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.9813923
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73123.636132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85315443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.281522
X-RAY DIFFRACTIONr_chiral_restr0.0830.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022245
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21404
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21959
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5591.51849
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89122863
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.70731190
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6724.51060
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.28 188 -
Rwork0.225 3597 -
obs--94.98 %
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)
11.0528-0.05830.03720.6285-0.05531.6195-0.0001-0.0058-0.02440.0430.0157-0.02590.03270.043-0.0156-0.1350.00350.0009-0.16410.0087-0.12226.17213.302717.7612
234.670423.4271-19.693740.2231.063319.65270.5317-1.22461.54010.4938-0.37710.6706-0.2897-0.4718-0.15460.00420.0097-0.00430.0117-0.00170.0035.490713.030118.4807
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 389
2X-RAY DIFFRACTION2A401

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