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- PDB-3t9m: Crystal structure of Mutant C221D of Carbapenemase CphA from Aero... -

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Basic information

Entry
Database: PDB / ID: 3t9m
TitleCrystal structure of 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 / 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
ACETATE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsDelbruck, H. / Hoffmann, K.M.V.
CitationJournal: To be Published
Title: Crystal structure of Mutant C221D of Carbapenemase CphA from Aeromonas Hydrophila
Authors: Delbruck, H. / Bebrone, C. / Hoffmann, K.M.V. / Galleni, M.
History
DepositionAug 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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_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)25,3513
Polymers25,2331
Non-polymers1182
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.605, 64.639, 67.140
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 277 K / pH: 4.6
Details: 0.05 M sodium acetate, 0.05 M potassium phosphate monobasic, 20% PEG8000, 100 nM zinc chloride, 1 mM EDTA, pH 4.6, VAPOR DIFFUSION, 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: May 26, 2009 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→19.29 Å / Num. obs: 14341 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 21.5 Å2 / Rsym value: 0.052 / Net I/σ(I): 16.7
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.25 / % possible all: 98.2

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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: 2.03→19.29 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.194 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 752 5.1 %RANDOM
Rwork0.179 ---
obs0.181 14052 99.5 %-
all-14804 --
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: 33.014 Å2
Baniso -1Baniso -2Baniso -3
1-5.28 Å20 Å20 Å2
2---1.56 Å20 Å2
3----3.72 Å2
Refinement stepCycle: LAST / Resolution: 2.03→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 8 170 1796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221694
X-RAY DIFFRACTIONr_bond_other_d0.0010.021140
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9572305
X-RAY DIFFRACTIONr_angle_other_deg0.85532789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2835209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79423.86775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2115282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.846159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211875
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02339
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_it0.4461.51039
X-RAY DIFFRACTIONr_mcbond_other0.1221.5418
X-RAY DIFFRACTIONr_mcangle_it0.75821684
X-RAY DIFFRACTIONr_scbond_it1.2723655
X-RAY DIFFRACTIONr_scangle_it2.0384.5619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 48 -
Rwork0.222 957 -
obs--95.62 %
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)
10.75760.93730.5883.08940.95523.0648-0.1205-0.18710.09350.070.00080.30430.1905-0.37590.11970.0852-0.012-0.00370.2196-0.01050.199727.000461.011719.593
21.02630.51680.22881.44860.09642.61080.0716-0.0496-0.01380.0685-0.0398-0.03350.44940.0395-0.03180.0970.00340.00040.08390.00540.105934.14256.340117.5989
36.47523.4197-5.18628.818-6.15485.8189-0.0617-0.1756-0.43-0.2595-0.09750.14770.17230.13550.15920.1702-0.0573-0.01880.07390.05490.11433.091547.234620.1583
40.879-0.0649-0.2171.71030.1693.1823-0.04260.0126-0.0159-0.01710.0333-0.02110.19760.11070.00940.03690.01390.00480.10340.00480.130239.892860.04829.8591
51.7832-1.241-1.14465.29413.722810.4520.12540.13970.21780.06260.098-0.3765-0.49950.4719-0.22340.0603-0.0350.00440.09670.03770.113243.692472.58249.7679
60.9149-0.6764-0.43731.8913-0.06984.02960.00160.1012-0.064-0.0501-0.0071-0.03440.39290.27350.00550.05950.04190.02510.05850.01380.079937.991958.88846.6295
71.25220.4956-0.04591.57260.03881.9916-0.0065-0.0208-0.0057-0.1899-0.07650.10270.0895-0.21550.0830.0333-0.019-0.0130.1346-0.01180.157126.732662.89332.5849
83.0495-0.9715-1.20646.41462.28495.84820.11740.17690.0598-0.2331-0.25490.3737-0.2873-0.65730.13750.02670.0223-0.04580.1953-0.02030.172819.391170.5534-0.1455
924.528814.945310.136212.55456.26149.29120.0223-1.02690.40480.4976-0.47930.8426-0.0608-1.19990.4570.1020.00580.02480.2346-0.0030.219219.46263.48369.1492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 68
2X-RAY DIFFRACTION2A69 - 97
3X-RAY DIFFRACTION3A98 - 109
4X-RAY DIFFRACTION4A110 - 139
5X-RAY DIFFRACTION5A140 - 161
6X-RAY DIFFRACTION6A162 - 187
7X-RAY DIFFRACTION7A188 - 218
8X-RAY DIFFRACTION8A219 - 253
9X-RAY DIFFRACTION9A254 - 264

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