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- PDB-3fai: The Di Zinc Carbapenemase CphA N220G mutant -

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Basic information

Entry
Database: PDB / ID: 3fai
TitleThe Di Zinc Carbapenemase CphA N220G mutant
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 / 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: 1.7 Å
AuthorsDelbruck, H. / Hoffmann, K.M.V.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2009
Title: The structure of the dizinc subclass B2 metallo-beta-lactamase CphA reveals that the second inhibitory zinc ion binds in the histidine site
Authors: Bebrone, C. / Delbruck, H. / Kupper, M.B. / Schlomer, P. / Willmann, C. / Frere, J.-M. / Fischer, R. / Galleni, M. / Hoffmann, K.M.V.
History
DepositionNov 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)26,55721
Polymers25,1641
Non-polymers1,39320
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,11442
Polymers50,3282
Non-polymers2,78640
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area7000 Å2
ΔGint-531 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.680, 101.060, 116.820
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-350-

HOH

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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, 271 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.4M (NH4)2SO4, 100mM MES, 100mM ZnCl2, 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: Mar 10, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→19.6 Å / Num. all: 28046 / Num. obs: 28035 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 11.96 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 42.1
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 25.6 / Num. unique all: 3970 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0053refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1x8g

1x8g


Resolution: 1.7→19.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.577 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.085 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16024 1403 5 %RANDOM
Rwork0.1388 26597 --
all0.13991 28000 --
obs0.13991 26597 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 61.06 Å2 / Biso mean: 7.841 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 63 251 2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221991
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9952736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82923.73583
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59315340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7381511
X-RAY DIFFRACTIONr_chiral_restr0.1260.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211492
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_it1.0631.51191
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63521958
X-RAY DIFFRACTIONr_scbond_it2.9043800
X-RAY DIFFRACTIONr_scangle_it4.2574.5759
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.704→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.173 88 -
Rwork0.133 1878 -
all-1966 -
obs--97.91 %
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)
10.6202-0.0292-0.0930.81720.08860.81460.0033-0.00230.02370.026-0.02630.0483-0.0302-0.07110.0230.01130.0075-0.00520.02690.00120.04127.26616.329-9.271
21.4348-0.40621.12551.9502-3.47987.4736-0.01910.0356-0.2112-0.1477-0.1328-0.01390.51540.08640.15190.1317-0.00220.02410.0578-0.01230.11518.863-2.307-13.243
30.4346-0.2368-0.09410.42780.00560.70240.02170.07310.0371-0.0684-0.0135-0.0119-0.0502-0.0345-0.00820.02610.007-0.00710.02470.00370.035613.16317.897-19.375
42.2190.0039-1.58531.14030.49593.6753-0.1389-0.0445-0.21390.12530.01920.03770.40460.16820.11970.09760.02380.01380.05840.00640.094325.2345.51-15.672
50.2354-0.0441-0.24180.56880.11611.34850.02180.02620.0365-0.01790.0332-0.0833-0.07350.1107-0.0550.015-0.0135-0.00390.0494-0.00760.055426.85818.987-15.049
63.4068-0.55170.25253.2031.45614.3833-0.04120.0514-0.09210.01260.1094-0.09620.21630.295-0.06820.0180.0273-0.00350.099-0.00690.056732.2989.982-14.264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 94
2X-RAY DIFFRACTION1A95 - 146
3X-RAY DIFFRACTION2A147 - 164
4X-RAY DIFFRACTION3A165 - 218
5X-RAY DIFFRACTION4A219 - 242
6X-RAY DIFFRACTION5A243 - 291
7X-RAY DIFFRACTION6A292 - 307

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