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- PDB-2wk0: Crystal structure of the class A beta-lactamase BS3 inhibited by ... -

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Basic information

Entry
Database: PDB / ID: 2wk0
TitleCrystal structure of the class A beta-lactamase BS3 inhibited by 6- beta-iodopenicillanate.
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / BETA- LACTAMASE / IODOPENICILLANATE / ANTIBIOTIC RESISTANCE / BACILLUS LICHENIFORMIS
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Beta-lactamase / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / 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-BIY / CITRIC ACID / ETHANOL / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesBACILLUS LICHENIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSauvage, E. / Zervosen, A. / Dive, G. / Herman, R. / Kerff, F. / Amoroso, A. / Fonze, E. / Pratt, R.F. / Luxen, A. / Charlier, P.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Structural Basis of the Inhibition of Class a Beta-Lactamases and Penicillin-Binding Proteins by 6-Beta-Iodopenicillanate.
Authors: Sauvage, E. / Zervosen, A. / Dive, G. / Herman, R. / Amoroso, A. / Joris, B. / Fonze, E. / Pratt, R.F. / Luxen, A. / Charlier, P. / Kerff, F.
History
DepositionJun 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)60,00412
Polymers59,0272
Non-polymers97810
Water6,557364
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0007
Polymers29,5131
Non-polymers4876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0045
Polymers29,5131
Non-polymers4914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.988, 104.479, 63.740
Angle α, β, γ (deg.)90.00, 94.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA-LACTAMASE


Mass: 29513.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BACILLUS LICHENIFORMIS (bacteria) / Strain: BS3
References: UniProt: P94458, UniProt: P00808*PLUS, beta-lactamase

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Non-polymers , 6 types, 374 molecules

#2: Chemical ChemComp-BIY / (3S)-2,2-dimethyl-3,4-dihydro-2H-1,4-thiazine-3,6-dicarboxylic acid


Mass: 217.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO4S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 50.91 % / Description: NONE
Crystal growpH: 3.4 / Details: pH 3.4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9474
DetectorDate: Nov 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9474 Å / Relative weight: 1
ReflectionResolution: 1.65→27 Å / Num. obs: 72436 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.7
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B3X

3b3x


Resolution: 1.65→17.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.286 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 3657 5.1 %RANDOM
Rwork0.1889 ---
obs0.19006 68715 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.606 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→17.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 58 364 4412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9945553
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99225.161186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28915740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0751528
X-RAY DIFFRACTIONr_chiral_restr0.0750.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023058
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.22065
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22886
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.2309
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3660.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5071.52621
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.83724108
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.68531653
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4294.51445
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: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 261 -
Rwork0.275 4984 -
obs--97.22 %
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)
11.9376-0.863-1.28421.47160.35251.9445-0.0464-0.22640.0440.3368-0.0647-0.2963-0.1550.33260.11110.0102-0.0541-0.06390.0529-0.00160.034334.421-3.345-0.262
21.1574-0.15860.34691.649-0.05111.25740.01840.0805-0.0434-0.17770.0120.21890.0708-0.0947-0.03040.0325-0.0065-0.02680.00570.00120.046613.483-11.178-19.286
30.4008-0.52620.75294.99852.35635.7781-0.0658-0.02970.1338-0.00930.04880.0356-0.14520.09620.01710.028-0.02080.00670.0430.01880.060920.653-0.291-19.532
41.72810.3684-0.01111.4696-0.49271.9742-0.0041-0.03010.1210.109-0.0097-0.0168-0.12590.04190.01380.06720.0104-0.0170.028-0.01090.070420.662-2.062-10.718
59.8263-4.2913-2.32383.81940.80062.2724-0.1573-0.2065-0.34530.14980.09360.3280.1485-0.22680.06370.0426-0.0195-0.00960.00760.0060.032513.71-16.631-6.434
62.62520.1019-0.37861.4792-0.31921.45610.0242-0.1792-0.08990.233-0.0469-0.1580.0260.18020.02270.0363-0.0017-0.03020.03680.01280.044830.205-12.073-4.655
70.6292-0.37790.88282.318-0.05721.3456-0.09420.1209-0.0513-0.23250.0974-0.113-0.02410.0653-0.00320.0482-0.03620.01910.0181-0.00170.032722.86110.16516.476
85.00413.852-0.2096.66422.19555.47090.0336-0.01870.34240.56110.42621.53990.1589-0.9668-0.4599-0.11690.13550.10970.16590.37110.4178-3.1697.70131.427
92.02050.6111-0.8764.1011-1.53983.5874-0.0589-0.0683-0.1710.07210.48250.6220.1671-0.6822-0.4236-0.1308-0.037-0.0030.07060.12790.17076.6852.56627.209
101.60290.26250.13232.3747-1.64293.0305-0.0401-0.0858-0.1589-0.03380.1417-0.02680.026-0.0438-0.10170.0339-0.0220.0119-0.00660.00910.042118.4823.18425.93
111.87920.35140.71043.2646-1.03672.9678-0.07990.1988-0.0013-0.39910.27770.50390.1448-0.3717-0.19790.0106-0.0457-0.04740.03430.04770.042910.77612.0313.823
122.01280.6969-0.27533.9453-1.34275.0357-0.06990.04230.10630.00350.0698-0.0786-0.27320.03610.00010.0697-0.0317-0.00580.00550.01840.06324.16119.70619.664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 63
2X-RAY DIFFRACTION2A64 - 157
3X-RAY DIFFRACTION3A158 - 167
4X-RAY DIFFRACTION4A168 - 201
5X-RAY DIFFRACTION5A202 - 217
6X-RAY DIFFRACTION6A218 - 290
7X-RAY DIFFRACTION7B31 - 81
8X-RAY DIFFRACTION8B82 - 120
9X-RAY DIFFRACTION9B121 - 156
10X-RAY DIFFRACTION10B157 - 194
11X-RAY DIFFRACTION11B195 - 265
12X-RAY DIFFRACTION12B266 - 290

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