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- PDB-3iog: Crystal structure of CphA N220G mutant with inhibitor 18 -

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Basic information

Entry
Database: PDB / ID: 3iog
TitleCrystal structure of CphA N220G mutant with inhibitor 18
ComponentsBeta-lactamase
KeywordsHYDROLASE / Antibiotic resistance / Metal-binding
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-SDF / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsDelbruck, H. / Bebrone, C. / Hoffmann, K.M.V.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Mercaptophosphonate Compounds as Broad-Spectrum Inhibitors of the Metallo-beta-lactamases
Authors: Lassaux, P. / Hamel, M. / Gulea, M. / Delbruck, H. / Mercuri, P.S. / Horsfall, L. / Dehareng, D. / Kupper, M. / Frere, J.-M. / Hoffmann, K. / Galleni, M. / Bebrone, C.
History
DepositionAug 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)26,16710
Polymers25,1641
Non-polymers1,0039
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.727, 100.877, 117.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-4-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 25163.768 Da / Num. of mol.: 1 / Mutation: N220G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: cphA / Plasmid: pET9a-CphA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys S / References: UniProt: P26918, beta-lactamase

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Non-polymers , 5 types, 294 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SDF / [(R)-(2,4-dichlorophenyl)(sulfanyl)methyl]phosphonic acid / alpha-Sulfanyl(2,4-dichlorobenzyl)phosphonic acid


Mass: 273.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7Cl2O3PS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS COORDINATES USE NON-SEQUENTIAL RESIDUE NUMBERING. THE NUMBERING RELATES TO PDB ENTRY 1X8G.

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.4M (NH4)2SO4, 100mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 29, 2008 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.41→19.67 Å / Num. all: 48494 / Num. obs: 48494 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 10.52 Å2 / Rsym value: 0.037 / Net I/σ(I): 37.3
Reflection shellResolution: 1.41→1.49 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 6754 / Rsym value: 0.1 / % possible all: 95.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X8G

1x8g


Resolution: 1.41→19.59 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.264 / SU ML: 0.025 / Isotropic thermal model: isotrpic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.051 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; remark 500 was generated for GLU 184 with zero occupancy and can be ignored
RfactorNum. reflection% reflectionSelection details
Rfree0.15474 2494 5.1 %RANDOM
Rwork0.14333 45999 --
obs0.14391 48493 98.33 %-
all-48494 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.243 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.41→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 52 285 2113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221978
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9982686
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.71123.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.30115364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9231510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211420
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_it0.6021.51156
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98621909
X-RAY DIFFRACTIONr_scbond_it1.6373822
X-RAY DIFFRACTIONr_scangle_it2.3824.5777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.411→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 161 -
Rwork0.143 3175 -
all-3336 -
obs-6754 92.92 %
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)
10.8451-0.2484-0.00761.6173-0.03230.96650.00430.06370.0645-0.1039-0.0173-0.0462-0.0520.01040.01310.0226-0.0089-0.00230.01080.00860.014210.71917.60763.794
20.80450.38170.01672.5038-1.34021.592-0.00490.01020.0562-0.1139-0.0944-0.1107-0.1010.14120.09930.0454-0.02030.00940.04450.0180.048920.12721.95160.672
31.23120.2699-0.03971.017-0.02191.2136-0.0158-0.02760.0067-0.0132-0.0147-0.0718-0.04130.14360.03050.0162-0.0119-0.01110.03120.01040.014416.70213.19272.343
40.82660.5190.1252.2351-0.19881.3849-0.0267-0.0549-0.01790.14860.0113-0.16290.08720.09810.01540.03940.0002-0.02130.04720.0060.025515.30410.13382.691
53.08970.38951.09093.27122.02787.8940.1093-0.1157-0.16910.1457-0.10530.00080.6893-0.2346-0.00390.115-0.02490.00530.01050.0030.019911.734-2.96672.4
60.61070.02190.10590.89570.10171.20290.015-0.0607-0.00150.0866-0.0221-0.11940.08160.11090.00710.0293-0.0154-0.01540.04620.00750.030715.50711.13476.119
70.68550.0732-0.05690.7103-0.31881.3634-0.0241-0.05090.04980.03570.01870.0076-0.0977-0.07920.00530.0254-0.0003-0.00540.0321-0.00430.0212.96719.35276.465
81.2566-0.2991-0.98642.22011.2582.2729-0.14980.0153-0.11820.0620.08990.02130.2012-0.18310.05990.0612-0.02590.00510.09080.01460.0492-5.238.8179.265
90.6731-0.4826-0.152.20760.40131.60660.00150.0050.006-0.01520.02130.0916-0.0923-0.1907-0.02280.00980.003-0.0070.04380.0180.0248-3.22519.73368.314
104.02730.8595-0.87494.9893-1.72074.881-0.13340.0665-0.1642-0.02280.1890.08460.3278-0.499-0.05570.0342-0.0615-0.00270.15610.01170.0407-10.5259.39873.617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 92
2X-RAY DIFFRACTION2A93 - 108
3X-RAY DIFFRACTION3A109 - 134
4X-RAY DIFFRACTION4A135 - 149
5X-RAY DIFFRACTION5A150 - 160
6X-RAY DIFFRACTION6A161 - 183
7X-RAY DIFFRACTION7A184 - 225
8X-RAY DIFFRACTION8A226 - 252
9X-RAY DIFFRACTION9A253 - 291
10X-RAY DIFFRACTION10A292 - 307

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