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- PDB-3sbl: Crystal Structure of New Delhi Metal-beta-lactamase-1 from Klebsi... -

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Basic information

Entry
Database: PDB / ID: 3sbl
TitleCrystal Structure of New Delhi Metal-beta-lactamase-1 from Klebsiella pneumoniae
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
CITRIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Binkowski, T.A. / Mire, J. / 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
DepositionJun 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2922
Polymers25,1001
Non-polymers1921
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase NDM-1
hetero molecules

A: Beta-lactamase NDM-1
hetero molecules

A: Beta-lactamase NDM-1
hetero molecules

A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1698
Polymers100,4014
Non-polymers7684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Buried area10010 Å2
ΔGint-36 kcal/mol
Surface area32520 Å2
MethodPISA
3
A: Beta-lactamase NDM-1
hetero molecules

A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5854
Polymers50,2002
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2240 Å2
ΔGint-16 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.050, 83.269, 105.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 25100.152 Da / Num. of mol.: 1 / 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): BM21 magic / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.8 M Ammonium citrate dibasic, 0.1 M Sodium acetate trihydrate pH 4.6, 10 mM aztreonam, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 12326 / Num. obs: 12326 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 36.45 Å2 / Rsym value: 0.091 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 528 / Rsym value: 0.334 / % possible all: 84.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_761)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3RKK

3rkk


Resolution: 2.31→36.923 Å / SU ML: 0.68 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 32.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.26 596 4.85 %random
Rwork0.2 ---
all0.203 12300 --
obs0.203 12300 93.93 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.585 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1--18.9206 Å20 Å20 Å2
2--2.3617 Å2-0 Å2
3---16.5589 Å2
Refinement stepCycle: LAST / Resolution: 2.31→36.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 13 61 1800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121800
X-RAY DIFFRACTIONf_angle_d1.522456
X-RAY DIFFRACTIONf_dihedral_angle_d16.639625
X-RAY DIFFRACTIONf_chiral_restr0.104270
X-RAY DIFFRACTIONf_plane_restr0.009327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3102-2.54260.42311140.30262499261381
2.5426-2.91040.25271570.25462983314097
2.9104-3.66630.31171530.19453065321899
3.6663-36.9280.20861720.16633157332998
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)
14.6534-0.0275-0.08273.6783-1.70894.4615-0.15720.4323-0.1042-0.24480.266-0.02310.0526-0.1347-0.04970.1907-0.02030.00960.37620.08190.3909-8.0321-18.2812-49.9851
24.89741.1958-1.12843.1524-0.08413.57210.18150.19260.22110.00020.10890.2502-0.1699-0.317-0.24510.18780.016-0.00180.2710.05780.318-13.637-15.8996-40.1375
38.1091-1.71120.67681.3942-0.83874.25650.09-0.49580.0953-0.0510.1786-0.0452-0.33140.174-0.28950.343-0.03150.08470.3084-0.03730.3381-6.427-16.9236-25.8326
47.17824.20830.37639.24791.93655.1065-0.3415-0.4050.08210.0647-0.01670.3634-0.0018-0.21410.33950.22450.0849-0.0050.3250.030.23761.8923-20.6758-37.7643
53.87251.74212.06582.8156-0.65.4249-0.35660.0920.76860.1199-0.0999-0.069-0.43680.32020.47510.23730.0304-0.04010.32840.05410.45019.1522-13.1311-35.2146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 38:67)
2X-RAY DIFFRACTION2chain 'A' and (resseq 68:137)
3X-RAY DIFFRACTION3chain 'A' and (resseq 138:194)
4X-RAY DIFFRACTION4chain 'A' and (resseq 195:212)
5X-RAY DIFFRACTION5chain 'A' and (resseq 213:269)

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