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- PDB-3s1y: AMP-C BETA-LACTAMASE (PSEUDOMONAS AERUGINOSA) in complex with a b... -

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Basic information

Entry
Database: PDB / ID: 3s1y
TitleAMP-C BETA-LACTAMASE (PSEUDOMONAS AERUGINOSA) in complex with a beta-lactamase inhibitor
ComponentsBeta-lactamase
KeywordsHydrolase/Hydrolase Inhibitor / Hydrolase / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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
ISOPROPYL ALCOHOL / Chem-S1Y / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsScapin, G. / Lu, J. / Fitzgerald, P.M.D. / Sharma, N.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Side chain SAR of bicyclic Beta-lactamase inhibitors (BLIs). 2. N-Alkylated and open chain analogs of MK-8712
Authors: Chen, H. / Blizzard, T.A. / Kim, S. / Wu, J. / Young, K. / Park, Y.W. / Ogawa, A.M. / Raghoobar, S. / Painter, R.E. / Wisniewski, D. / Hairston, N. / Fitzgerald, P. / Sharma, N. / Scapin, G. ...Authors: Chen, H. / Blizzard, T.A. / Kim, S. / Wu, J. / Young, K. / Park, Y.W. / Ogawa, A.M. / Raghoobar, S. / Painter, R.E. / Wisniewski, D. / Hairston, N. / Fitzgerald, P. / Sharma, N. / Scapin, G. / Lu, J. / Hermes, J. / Hammond, M.L.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Oct 30, 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 / _pdbx_entry_details.has_protein_modification / _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)41,1715
Polymers40,6381
Non-polymers5334
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.253, 69.696, 101.667
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: 40637.848 Da / Num. of mol.: 1 / Mutation: R397A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ampC, PA4110 / Plasmid: pET 26 / Production host: Escherichia coli (E. coli) / References: UniProt: P24735, beta-lactamase
#2: Chemical ChemComp-S1Y / [(2S,3R)-1-{[(4S)-1-(2-aminoethyl)azepan-4-yl]carbamoyl}-2-formylpyrrolidin-3-yl]sulfamic acid


Mass: 377.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H27N5O5S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE STARTING MATERIAL IS A CLOSED RING BETA-LACTAMASE INHIBITOR, THAT REACTS WITH SER90 TO BECOME ...THE STARTING MATERIAL IS A CLOSED RING BETA-LACTAMASE INHIBITOR, THAT REACTS WITH SER90 TO BECOME THE OPEN RING COMPOUND, S1Y

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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: 1.89 Å3/Da / Density % sol: 34.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 3350, 10% 2-propanol, 100 mM Imidazole, microseeding, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 2, 2007
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→99 Å / Num. all: 75040 / Num. obs: 74960 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.2
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1 / Num. unique all: 12346 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MERLOTphasing
REFMAC5.5.0102refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.392 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20241 2927 5.1 %RANDOM
Rwork0.18103 ---
obs0.18214 54755 93.85 %-
all-58250 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.657 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.59 Å2
Refine analyzeLuzzati coordinate error obs: 0.196 Å
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 34 425 3227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222951
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.9854036
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06923.481135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64815456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7551524
X-RAY DIFFRACTIONr_chiral_restr0.0660.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212311
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.411.51833
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70922934
X-RAY DIFFRACTIONr_scbond_it1.31631118
X-RAY DIFFRACTIONr_scangle_it24.51090
X-RAY DIFFRACTIONr_rigid_bond_restr0.52232951
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 183 -
Rwork0.255 3715 -
obs--86.89 %
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)
10.8018-0.02990.07880.6240.00111.3544-0.0059-0.01270.00670.03120.0002-0.0159-0.00350.04330.00570.01070.00190.00210.00250.00350.02196.013.13817.228
252.006826.90822.484732.31431.690317.4833-0.14530.48751.2187-0.31490.2219-0.0365-0.38890.5104-0.07660.0556-0.0050.00130.03150.01050.0556.45313.12217.581
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 388
2X-RAY DIFFRACTION2A398

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