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- PDB-3rkj: Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Kleb... -

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Basic information

Entry
Database: PDB / ID: 3rkj
TitleCrystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pnueumoniae
ComponentsBeta-lactamase NDM-1
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta structure / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI
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 / 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 speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Binkowski, T.A. / Babnigg, G. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: Plos One / Year: 2011
Title: Structure of Apo- and Monometalated Forms of NDM-1 A Highly Potent Carbapenem-Hydrolyzing Metallo-beta-Lactamase
Authors: Kim, Y. / Tesar, C. / Mire, J. / Jedrzejczak, R. / Binkowski, A. / Babnigg, G. / Sacchettini, J. / Joachimiak, A.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 28, 2011Group: Experimental preparation
Revision 1.4Mar 28, 2012Group: Database references
Revision 1.5Sep 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 NDM-1
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2188
Polymers49,6462
Non-polymers5726
Water4,720262
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1074
Polymers24,8231
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1114
Polymers24,8231
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.712, 51.113, 70.680
Angle α, β, γ (deg.)90.00, 106.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase NDM-1 / NDM-1 / Metallo-beta-lactamase NDM-1


Mass: 24822.877 Da / Num. of mol.: 2 / Fragment: sequence database residues 39-270
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
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.17 M Ammonium sulfate 25.5 % (w/v) PEG 4000, 15 % (v/v) Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, 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: Apr 11, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / 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: 26835 / Num. obs: 26835 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 25.89 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 6.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1377 / % possible all: 96.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
BALBESphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2YZ3

2yz3


Resolution: 2→38.449 Å / SU ML: 0.22 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1335 5.06 %random
Rwork0.192 ---
all0.195 26368 --
obs0.195 26368 94.84 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.16 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.5039 Å20 Å2-4.5654 Å2
2---0.1148 Å20 Å2
3----1.3891 Å2
Refinement stepCycle: LAST / Resolution: 2→38.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 31 262 3653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013573
X-RAY DIFFRACTIONf_angle_d1.2354880
X-RAY DIFFRACTIONf_dihedral_angle_d14.5181238
X-RAY DIFFRACTIONf_chiral_restr0.1536
X-RAY DIFFRACTIONf_plane_restr0.007647
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2-2.07150.27871780.20532505268396
2.0715-2.15440.29211210.20242510263197
2.1544-2.25250.30261220.19692542266496
2.2525-2.37120.30181400.20422517265796
2.3712-2.51970.29661190.19082547266696
2.5197-2.71420.22361240.19732526265096
2.7142-2.98730.26941390.22500263995
2.9873-3.41930.24451340.18012483261794
3.4193-4.30710.18931260.17372438256492
4.3071-38.45640.22451320.19952465259791
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)
10.468-0.37130.37140.3245-0.22370.8403-0.12220.03360.1311-0.0362-0.1643-0.2382-0.0515-0.00150.13830.14540.0387-0.01340.1408-0.00090.1803-34.508412.618631.0748
20.87110.2235-0.01420.8550.18920.0457-0.13740.2820.0383-0.19250.03370.0958-0.03280.00390.03390.1448-0.0138-0.0215-0.03350.09340.0393-34.09039.216518.9872
30.43780.1899-0.35250.97160.03330.34040.00480.04740.00530.2054-0.04490.0871-0.07050.1691-0.0080.1032-0.00560.01530.12020.00430.0695-28.46644.418130.2467
40.6639-0.3404-0.01030.6362-0.38860.54370.01620.01590.0652-0.09360.0229-0.04250.1203-0.1666-0.00930.0915-0.0092-0.00330.101-0.00270.1024-24.2668.840927.3948
50.6502-0.17620.22690.5993-0.14330.82520.1612-0.1226-0.4583-0.20.15250.15380.12880.167-0.05620.04360.11690.1121-0.2772-0.3496-0.1609-17.34-4.459821.1894
60.51180.0118-0.30730.38140.09520.4165-0.2247-0.04780.22850.0049-0.0646-0.03860.04020.09980.09360.00390.0262-0.01980.1471-0.04150.1198-23.814-10.17127.4742
70.8070.043-0.21590.35180.33480.5493-0.1211-0.1344-0.02470.1148-0.07040.13350.0818-0.03210.07830.1308-0.04290.03930.11-0.02060.1341-34.5165-6.163227.2293
81.00630.1138-0.22550.0386-0.19120.9432-0.30320.2193-0.0247-0.0148-0.0325-0.0649-0.1506-0.23790.10150.19390.0246-0.00910.2447-0.02650.1969-35.4821-11.14112.0106
90.48930.1312-0.0020.6205-0.14920.2909-0.16540.0457-0.0233-0.12060.08480.15880.06650.0760.03770.1031-0.01880.0080.0815-0.0020.0715-37.8182-9.285125.3755
100.5597-0.3468-0.68330.99281.11792.2799-0.05550.3077-0.1773-0.21450.03990.029-0.2324-0.34260.04620.1344-0.0455-0.01350.1935-0.03290.1184-41.5512-15.190616.926
110.3475-0.16490.19810.18750.10960.45280.18170.04110.1058-0.0242-0.2687-0.20120.22330.00650.04360.18960.02110.0435-0.2955-0.0410.2125-2.578813.95884.6297
120.34330.1045-0.27510.5072-0.1460.32810.07580.0746-0.0862-0.0955-0.036-0.1892-0.0866-0.1152-0.01380.0743-0.0045-0.03120.0379-0.04420.0708-10.026917.92457.138
130.34690.24470.0140.2680.30720.5539-0.09350.0135-0.0054-0.0350.03110.00790.0938-0.04550.04880.10980.01530.0180.09090.00950.1392-8.864615.457514.7601
140.9992-0.36010.00090.7788-0.11230.5028-0.0847-0.3366-0.3438-0.09340.02440.3056-0.21730.05680.0431-0.00930.094-0.02610.06860.01940.1044-16.416228.641420.3031
150.24450.07580.12060.60820.31681.0867-0.0238-0.0263-0.04910.13920.051-0.02340.1648-0.24970.01120.1129-0.0091-0.03360.1328-0.02680.0992-9.178734.331115.0358
160.6701-0.3291-0.20610.76850.190.34150.1180.0920.0009-0.1256-0.0927-0.1047-0.0045-0.0392-0.03560.13460.02570.02560.1162-0.00460.119-6.909330.49572.4998
170.33270.09920.04740.55470.15570.5272-0.0082-0.01320.1305-0.0525-0.06880.1344-0.0185-0.11970.050.1167-0.0442-0.01670.1457-0.03090.1041-19.292537.8172.9433
180.74080.18220.07040.52310.26580.36640.2330.0695-0.0042-0.14980.14020.00950.0231-0.0253-0.07680.1593-0.0059-0.01860.10440.01690.0919-6.575529.662-0.2397
195.0851-1.09060.02840.7651-0.15870.3168-0.25710.36890.05990.13480.1503-0.0237-0.1579-0.07970.10290.12720.02720.03380.11190.02260.0772-16.500339.6184-4.0962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 45:57)
2X-RAY DIFFRACTION2chain 'A' and (resseq 58:73)
3X-RAY DIFFRACTION3chain 'A' and (resseq 74:94)
4X-RAY DIFFRACTION4chain 'A' and (resseq 95:137)
5X-RAY DIFFRACTION5chain 'A' and (resseq 138:166)
6X-RAY DIFFRACTION6chain 'A' and (resseq 167:194)
7X-RAY DIFFRACTION7chain 'A' and (resseq 195:212)
8X-RAY DIFFRACTION8chain 'A' and (resseq 213:228)
9X-RAY DIFFRACTION9chain 'A' and (resseq 229:255)
10X-RAY DIFFRACTION10chain 'A' and (resseq 256:270)
11X-RAY DIFFRACTION11chain 'B' and (resseq 45:57)
12X-RAY DIFFRACTION12chain 'B' and (resseq 58:94)
13X-RAY DIFFRACTION13chain 'B' and (resseq 95:137)
14X-RAY DIFFRACTION14chain 'B' and (resseq 138:166)
15X-RAY DIFFRACTION15chain 'B' and (resseq 167:194)
16X-RAY DIFFRACTION16chain 'B' and (resseq 195:215)
17X-RAY DIFFRACTION17chain 'B' and (resseq 216:239)
18X-RAY DIFFRACTION18chain 'B' and (resseq 240:255)
19X-RAY DIFFRACTION19chain 'B' and (resseq 256:270)

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