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- PDB-6ex7: Crystal structure of NDM-1 metallo-beta-lactamase in complex with... -

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Basic information

Entry
Database: PDB / ID: 6ex7
TitleCrystal structure of NDM-1 metallo-beta-lactamase in complex with Cd ions and a hydrolyzed beta-lactam ligand - new refinement
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / NDM-1 / metallo-beta-lactamase
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
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Unknown ligand / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsKim, Y. / Raczynska, J.E. / Shabalin, I.G. / Jaskolski, M. / Minor, W. / Wlodawer, A. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Mire, J. ...Kim, Y. / Raczynska, J.E. / Shabalin, I.G. / Jaskolski, M. / Minor, W. / Wlodawer, A. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Mire, J. / Sacchettini, J. / Joachimiak, A.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Center for Research and DevelopmentDesInMBL Poland
Citation
Journal: Drug Resist. Updat. / Year: 2018
Title: A close look onto structural models and primary ligands of metallo-beta-lactamases.
Authors: Raczynska, J.E. / Shabalin, I.G. / Minor, W. / Wlodawer, A. / Jaskolski, M.
#1: Journal: FASEB J. / Year: 2013
Title: NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism.
Authors: Kim, Y. / Cunningham, M.A. / Mire, J. / Tesar, C. / Sacchettini, J. / Joachimiak, A.
History
DepositionNov 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3May 8, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_asym_id / _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_asym_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_asym_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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,01616
Polymers51,4362
Non-polymers1,58014
Water3,207178
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5868
Polymers25,7181
Non-polymers8697
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4298
Polymers25,7181
Non-polymers7117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.062, 39.220, 75.233
Angle α, β, γ (deg.)90.00, 99.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-306-

PG4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 31 - 269 / Label seq-ID: 4 - 242

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 25717.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: C7C422, beta-lactamase

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Non-polymers , 7 types, 192 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 189.189 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25 % PEG 3350, 5 mM CdCl2,10 mM faropenum, temperature 289K
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.95→74.2 Å / Num. obs: 27008 / % possible obs: 91.72 % / Redundancy: 2.9 % / Net I/σ(I): 15.6
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.2 / % possible all: 66

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementResolution: 1.95→74.2 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.225 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.221 / ESU R Free: 0.171 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22588 1353 4.8 %copied from entry 4hky
Rwork0.1945 ---
obs0.19608 27008 91.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.627 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å2-0 Å20.59 Å2
2---1.25 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.95→74.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 55 178 3731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193649
X-RAY DIFFRACTIONr_bond_other_d0.0050.023374
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9394929
X-RAY DIFFRACTIONr_angle_other_deg1.1693.0017710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51624.726146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17415506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9451514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214275
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02827
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_it2.1691.3091922
X-RAY DIFFRACTIONr_mcbond_other2.1671.3091921
X-RAY DIFFRACTIONr_mcangle_it3.0441.952399
X-RAY DIFFRACTIONr_mcangle_other3.0441.952400
X-RAY DIFFRACTIONr_scbond_it3.5681727
X-RAY DIFFRACTIONr_scbond_other3.561727
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8262.3262531
X-RAY DIFFRACTIONr_long_range_B_refined6.9553971
X-RAY DIFFRACTIONr_long_range_B_other6.9593972
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded29.6856
Refine LS restraints NCS

Ens-ID: 1 / Number: 25944 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2 Å
RfactorNum. reflection% reflection
Rwork0.213 1481 -
Rfree-0 -
obs--66 %
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)
17.97392.74921.93788.75085.21943.1273-0.11060.74040.3376-0.1657-0.22330.5326-0.0808-0.09430.3340.7981-0.1702-0.05310.2630.07030.06316.08329.325-10.561
210.27750.49112.57513.451.11874.61510.0419-0.0731-0.388-0.91210.01430.1461-0.8419-0.148-0.05620.42320.0141-0.05070.09780.01250.023818.10325.433-2.56
35.14340.311.44571.32973.44989.5338-0.01240.605-0.1756-0.76060.0230.0107-1.6090.2631-0.01060.6810.0363-0.01110.1521-0.01880.013821.63619.472-4.03
41.056-0.04110.04162.49521.45343.245-0.08860.1184-0.0069-0.48090.00910.0413-0.55680.06830.07950.1483-0.0249-0.05060.1203-0.0060.0918.61924.86410.163
59.97340.4689-4.83553.1769-1.27026.74850.1383-0.31430.641-0.3866-0.36470.7412-0.6059-0.5790.22640.20640.1335-0.22260.3125-0.21070.3815.05636.41811.662
611.29510.00691.28118.6034-2.03822.7405-0.0813-0.5103-0.2584-0.20850.02170.33450.0867-0.11710.05960.0257-0.00830.01630.22460.0480.06381.49711.90752.69
72.54560.0130.1522.52820.03092.0858-0.0449-0.2740.05860.39830.02180.15190.0102-0.04020.02310.09170.0530.00010.20960.01340.096911.29915.31547.644
80.8953-0.143-0.12411.88550.26751.7173-0.0562-0.1321-0.05110.14260.00060.0146-0.02440.04040.05560.02360.0184-0.03090.18280.0070.139816.40716.60934.652
92.7472-0.6901-0.05391.9756-0.00412.64-0.0517-0.0112-0.20590.0584-0.05480.26040.16-0.18770.10650.0133-0.02250.00610.1455-0.03630.20826.0976.28329.761
1012.8455-1.57261.952315.9848-5.458115.28080.11520.6980.0673-0.8611-0.091-0.06550.5162-0.2218-0.02420.0773-0.0154-0.0260.1875-0.06230.188-0.9575.6720.954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 56
2X-RAY DIFFRACTION2A57 - 86
3X-RAY DIFFRACTION3A87 - 105
4X-RAY DIFFRACTION4A106 - 251
5X-RAY DIFFRACTION5A252 - 270
6X-RAY DIFFRACTION6B30 - 52
7X-RAY DIFFRACTION7B53 - 108
8X-RAY DIFFRACTION8B109 - 215
9X-RAY DIFFRACTION9B216 - 262
10X-RAY DIFFRACTION10B263 - 270

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