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- PDB-4hky: New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem -

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Basic information

Entry
Database: PDB / ID: 4hky
TitleNew Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem
ComponentsBeta-lactamase NDM-1
KeywordsHydrolase/Antibiotic / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / alpha-beta-beta-alpha sandwich / hydrolase / PSI-Biology / Hydrolase-Antibiotic complex
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 / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-FPM / Chem-SFR / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Mire, J. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Mire, J. / Sacchettini, J. / Joachimiak, A.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Non-polymer description
Revision 1.2Sep 20, 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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.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_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 NDM-1
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,61418
Polymers51,4362
Non-polymers2,17816
Water2,450136
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7158
Polymers25,7181
Non-polymers9977
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,89910
Polymers25,7181
Non-polymers1,1819
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-57 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.627, 39.324, 75.370
Angle α, β, γ (deg.)90.00, 99.96, 90.00
Int Tables number5
Space group name H-MC121
Detailstwo monomers in the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase NDM-1 / NDM-1 / Metallo-beta-lactamase 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 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: C7C422, beta-lactamase

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Non-polymers , 6 types, 152 molecules

#2: Chemical ChemComp-FPM / (5R,6S)-6-(1-hydroxyethyl)-7-oxo-3-[(2R)-oxolan-2-yl]-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid / Faropenem


Mass: 285.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO5S / Comment: antibiotic*YM
#3: Chemical ChemComp-SFR / (2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid / FAROPENEM, unbound, hydrolyzed form


Mass: 303.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17NO6S / Comment: antibiotic*YM
#4: Chemical
ChemComp-CD / CADMIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 289 K / pH: 5.5
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

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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 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 28649 / Num. obs: 28649 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 32.08 Å2 / Rsym value: 0.103 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.629 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3QX6

3qx6
PDB Unreleased entry


Resolution: 2.004→37.117 Å / SU ML: 0.27 / Isotropic thermal model: mixed / σ(F): 1.33 / Phase error: 29.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 1446 5.06 %
Rwork0.2041 --
obs0.2066 28604 99.49 %
all-28604 -
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.9 Å2
Refinement stepCycle: LAST / Resolution: 2.004→37.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 77 136 3700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093633
X-RAY DIFFRACTIONf_angle_d1.7394949
X-RAY DIFFRACTIONf_dihedral_angle_d16.1111272
X-RAY DIFFRACTIONf_chiral_restr0.528553
X-RAY DIFFRACTIONf_plane_restr0.007657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0035-2.07510.36261430.28322673X-RAY DIFFRACTION98
2.0751-2.15820.30061190.25642676X-RAY DIFFRACTION99
2.1582-2.25640.31651400.232687X-RAY DIFFRACTION100
2.2564-2.37540.29591440.2272706X-RAY DIFFRACTION100
2.3754-2.52420.25231330.22252711X-RAY DIFFRACTION100
2.5242-2.7190.23711380.21712723X-RAY DIFFRACTION100
2.719-2.99250.24541650.20772709X-RAY DIFFRACTION100
2.9925-3.42530.251460.20612725X-RAY DIFFRACTION100
3.4253-4.31450.24381560.17862742X-RAY DIFFRACTION100
4.3145-37.12350.22451620.18572806X-RAY DIFFRACTION99
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)
10.64050.6458-0.52441.5333-0.05430.6912-0.14650.36020.1153-0.85130.06520.15210.1479-0.1525-0.29032.0111-0.26630.09990.30590.38990.007527.100630.2612-46.4928
20.8181-1.2918-0.53114.02420.61732.83450.12420.31090.045-1.7574-0.02570.184-1.30080.38080.03740.8627-0.08680.05230.33640.00320.216825.635424.2642-38.8944
35.72811.6983-1.84873.159-1.55451.0118-0.05380.87320.1403-1.48140.38890.1115-0.45910.6671-0.15420.8418-0.18570.13330.5063-0.02360.287733.81620.5984-42.2306
43.15760.5038-1.5244.29171.30057.7479-0.25420.291-0.3976-0.56940.0056-0.03980.2910.15750.27150.2272-0.02250.05220.2091-0.04880.237626.890315.4735-29.4422
52.53651.37721.93048.6636.49889.02830.0919-0.06560.0020.0361-0.24360.3070.0548-0.0930.07230.18550.01550.06080.13890.02680.227128.159618.7935-21.3965
66.3315-1.67731.2234.0294-0.55563.0544-0.13850.7970.1446-0.67040.0727-0.0762-0.91150.30530.04490.5924-0.06190.00650.2527-0.05240.238726.618128.7501-25.4079
76.2271-0.43941.1792.1657-1.1911.18860.01830.0370.0813-0.3277-0.28340.6949-0.5758-0.60060.23960.51890.1602-0.08680.3723-0.14560.353812.617230.0453-23.058
81.1351-1.3753-0.32352.56090.24550.11580.33720.47670.4743-0.6885-0.49070.4397-0.96660.21310.05661.29050.0702-0.08330.28960.04050.405621.593836.2186-31.8373
93.91431.607-0.14833.09442.38322.5143-0.2979-0.31310.28930.3462-0.26360.68870.2693-0.5562-0.16310.99440.2788-0.25870.2498-0.05690.575310.123336.0212-23.3459
107.6523-3.74330.71096.32.29165.0244-0.2932-0.3689-0.71510.7739-0.16011.3649-0.0423-0.39250.47080.72470.02440.13810.94240.13660.56146.387711.935316.0927
114.5086-1.14420.76952.38231.15784.28210.082-0.1795-0.02370.5935-0.03070.81150.2093-0.3177-0.01480.45820.03210.29840.35640.04220.515512.576712.6249.9729
123.14762.03060.98763.58710.54954.2367-0.0943-0.3393-0.43530.8035-0.02820.30170.31320.12860.04980.50780.10810.11670.28590.05420.210720.179514.57197.5549
134.6849-0.49971.64055.6639-0.40495.3233-0.3242-0.80880.27391.14120.4071-0.0546-0.0463-0.3081-0.07610.38810.12290.03580.3826-0.00660.246323.050318.234714.0911
142.5708-1.524-1.07814.62440.10737.6053-0.25-0.1815-0.07950.42810.15530.198-0.3583-0.1120.09480.210.03740.03330.1725-0.02120.228121.586323.6401-0.3339
153.719-2.756-3.19483.05734.0145.96220.02560.23530.24280.1794-0.0728-0.0409-0.090.039-0.01460.1891-0.00420.02640.20130.04770.253425.619520.2782-7.4436
164.8602-1.38620.69892.9040.36324.23680.0603-0.57230.38650.1719-0.031-0.090.2576-0.2674-0.03880.14240.01190.08660.12330.01650.215125.315613.4584-6.4388
176.98782.84182.1065.8303-0.00613.6960.1027-0.7348-0.39110.3103-0.24310.04050.6145-0.20640.21920.3490.0370.12820.29960.04770.279118.83676.04-1.0939
183.99740.19340.411.38030.23173.6426-0.0821-0.1791-0.35380.2874-0.06320.61040.2027-0.33410.11040.3073-0.01380.16460.2632-0.02930.387912.39726.7826-6.9045
198.4282-3.70685.40785.2556-3.26818.33260.31010.3351-1.2697-0.6686-0.12520.73190.7203-0.5472-0.11210.357-0.02490.0750.3523-0.14230.52357.92983.227-12.1509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 170 )
6X-RAY DIFFRACTION6chain 'A' and (resid 171 through 212 )
7X-RAY DIFFRACTION7chain 'A' and (resid 213 through 239 )
8X-RAY DIFFRACTION8chain 'A' and (resid 240 through 255 )
9X-RAY DIFFRACTION9chain 'A' and (resid 256 through 270 )
10X-RAY DIFFRACTION10chain 'B' and (resid 30 through 48 )
11X-RAY DIFFRACTION11chain 'B' and (resid 49 through 70 )
12X-RAY DIFFRACTION12chain 'B' and (resid 71 through 94 )
13X-RAY DIFFRACTION13chain 'B' and (resid 95 through 118 )
14X-RAY DIFFRACTION14chain 'B' and (resid 119 through 149 )
15X-RAY DIFFRACTION15chain 'B' and (resid 150 through 170 )
16X-RAY DIFFRACTION16chain 'B' and (resid 171 through 194 )
17X-RAY DIFFRACTION17chain 'B' and (resid 195 through 212 )
18X-RAY DIFFRACTION18chain 'B' and (resid 213 through 255 )
19X-RAY DIFFRACTION19chain 'B' and (resid 256 through 270 )

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