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- PDB-3sw3: EDTA-free crystal structure of the mutant C221D of carbapenemase ... -

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Basic information

Entry
Database: PDB / ID: 3sw3
TitleEDTA-free crystal structure of the mutant C221D of carbapenemase CphA from Aeromonas hydrophila
ComponentsBeta-lactamase
KeywordsHYDROLASE
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDelbruck, H. / Hoffmann, K.M.V.
CitationJournal: To be Published
Title: EDTA-free crystal structure of the mutant C221D of carbapenemase CphA from Aeromonas hydrophila
Authors: Delbruck, H. / Bebrone, C. / Hoffmann, K.M.V. / Galleni, M.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)25,2331
Polymers25,2331
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.622, 65.021, 67.272
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 / / carbapenemase CphA


Mass: 25232.764 Da / Num. of mol.: 1 / Fragment: UNP residues 28-254 / Mutation: C221D
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) pLysS / References: UniProt: P26918, beta-lactamase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 277 K / pH: 4.6
Details: 0.05 M sodium acetate, 0.05 M potassium phosphate monobasic, 20% PEG8000, 2 mM zinc chloride, pH 4.6, 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
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 9, 2009 / 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: 2.35→19.61 Å / Num. obs: 9845 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 33.33 Å2 / Rsym value: 0.069 / Net I/σ(I): 16.3
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.264 / % possible all: 98.6

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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: 2.35→19.61 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.883 / SU B: 17.893 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 469 4.8 %RANDOM
Rwork0.189 ---
obs0.192 9323 99 %-
all-9802 --
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: 42.695 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å20 Å2
2---0.47 Å20 Å2
3----3.15 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 0 110 1723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221673
X-RAY DIFFRACTIONr_bond_other_d00.021127
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9582280
X-RAY DIFFRACTIONr_angle_other_deg1.04332756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1415210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27323.91974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24215277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.951159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
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_it0.7461.51028
X-RAY DIFFRACTIONr_mcbond_other0.2091.5417
X-RAY DIFFRACTIONr_mcangle_it1.2721670
X-RAY DIFFRACTIONr_scbond_it2.1413645
X-RAY DIFFRACTIONr_scangle_it3.2174.5607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 41 -
Rwork0.186 653 -
obs--97.88 %
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)
10.77580.9-0.8152.6571-1.43152.4616-0.0107-0.1831-0.05480.10380.0463-0.114-0.12020.2305-0.03560.1364-0.009-0.00270.2125-0.01080.183523.994.98818.303
21.28060.69920.33471.59421.85160.24450.0492-0.0380.00050.031-0.03410.0145-0.0582-0.0713-0.01520.17510.00820.00410.1813-0.00220.164615.3027.60118.711
36.53380.37434.32794.36384.01912.0536-0.0022-0.14690.2215-0.3155-0.18860.0601-0.07610.31860.19070.2668-0.03560.00060.1985-0.02730.114518.64917.4520.756
40.85990.8328-0.4678-0.07350.33441.801-0.0604-0.0285-0.0085-0.0670.10360.0591-0.118-0.0952-0.04320.19930.0315-0.0050.1861-0.00560.156311.4784.99811.96
51.8881.8053-0.47941.3586-2.84844.6363-0.03550.1471-0.1049-0.1959-0.11350.00310.1703-0.26050.1490.14260.017-0.00820.2149-0.02710.19477.009-2.8363.619
66.5706-3.64483.06858.5878-3.47453.6989-0.0819-0.4095-0.35420.02790.37560.1760.3065-0.3566-0.29380.1493-0.04680.00910.163-0.02090.12437.382-8.98817.478
72.2731-0.49551.28922.3905-0.10292.25510.3140.3058-0.0945-0.2118-0.1549-0.0519-0.4505-0.2382-0.15910.25840.0442-0.02440.14650.00260.122913.1618.8591.165
89.01592.5387.346619.5203-22.85113.2537-0.37290.51820.4261-0.624-0.1841-0.6995-0.15640.78890.55690.2765-0.03280.04770.1030.02960.187423.72413.6192.092
9-0.823-1.4013-0.38040.61591.20941.06620.0588-0.0322-0.0698-0.2031-0.1112-0.1022-0.03950.11760.05240.1595-0.0219-0.00520.2020.00860.188424.0341.5162.507
105.72-3.1869-3.76419.5697-2.15316.8914-0.1401-0.12580.05740.2855-0.191-0.75230.20270.36930.33110.0597-0.0123-0.01630.20910.02830.202532.25-3.5456.544
113.495-0.35211.82662.2157-1.10023.5591-0.03560.3059-0.1719-0.16010.0632-0.07960.50350.2866-0.02750.13730.04140.05570.1930.00810.170229.841-8.509-1.272
125.07860.6312-5.30823.1904-0.046614.20150.04860.0302-0.19660.0991-0.1517-0.4309-0.18130.67110.1031-0.0124-0.01810.00560.1817-0.01180.206931.7781.2334.195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 76
2X-RAY DIFFRACTION2A77 - 98
3X-RAY DIFFRACTION3A99 - 109
4X-RAY DIFFRACTION4A110 - 136
5X-RAY DIFFRACTION5A137 - 152
6X-RAY DIFFRACTION6A153 - 170
7X-RAY DIFFRACTION7A171 - 183
8X-RAY DIFFRACTION8A184 - 189
9X-RAY DIFFRACTION9A190 - 216
10X-RAY DIFFRACTION10A217 - 231
11X-RAY DIFFRACTION11A232 - 249
12X-RAY DIFFRACTION12A250 - 264

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