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- PDB-5xp9: Crystal structure of Bismuth bound NDM-1 -

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Basic information

Entry
Database: PDB / ID: 5xp9
TitleCrystal structure of Bismuth bound NDM-1
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / antibiotics resistance / beta-lactamase / metallodrug / Bismuth
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; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bismuth(III) ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsZhang, H. / Ma, G. / Lai, T.P. / Sun, H.
CitationJournal: Nat Commun / Year: 2018
Title: Bismuth antimicrobial drugs serve as broad-spectrum metallo-beta-lactamase inhibitors
Authors: Wang, R. / Lai, T.P. / Gao, P. / Zhang, H. / Ho, P.L. / Woo, P.C. / Ma, G. / Kao, R.Y. / Li, H. / Sun, H.
History
DepositionJun 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,0203
Polymers25,7191
Non-polymers3012
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-0 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.595, 60.185, 41.796
Angle α, β, γ (deg.)90.00, 98.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: 25718.900 Da / Num. of mol.: 1 / Fragment: UNP residues 29-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pRHisMBP
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Strain (production host): BL21(DE3) / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-BS3 / Bismuth(III) ION


Mass: 208.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Bi
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.01 Å3/Da / Density % sol: 38.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH5.5, 15%PEG33500, 20mM L-Proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 28178 / % possible obs: 95.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.6
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.697 / % possible all: 94.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZOdata collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6X

3q6x
PDB Unreleased entry


Resolution: 1.55→41.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.876 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1387 5 %RANDOM
Rwork0.163 ---
obs0.164 26225 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.19 Å2
2---0.03 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.55→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 7 206 1910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191789
X-RAY DIFFRACTIONr_bond_other_d0.0020.021684
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.932445
X-RAY DIFFRACTIONr_angle_other_deg0.9333866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1015241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80424.4379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87315269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.66159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212110
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 86 -
Rwork0.227 1576 -
obs--76.06 %
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)
10.98950.3614-0.65612.5560.76950.86030.0713-0.20680.0240.1874-0.0860.06380.02320.12580.01470.0817-0.03240.00240.0654-0.0180.014932.68133.83940.113
20.12110.1097-0.21391.4954-0.03640.49850.0128-0.0554-0.028-0.0942-0.0721-0.1316-0.02160.04650.05930.03920.00020.0050.0530.00570.043337.81925.63428.803
31.0676-0.362-0.10030.9366-0.07490.61550.0015-0.00050.0282-0.11020.02750.28480.03570.0214-0.02890.0162-0.0074-0.03840.03550.00530.108320.96129.69126.242
43.89241.5381-7.10933.4804-5.085814.78960.32690.28580.3344-0.17040.1595-0.0223-0.3596-0.5567-0.48640.08390.00650.0010.04110.05330.118513.14238.70417.355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 70
2X-RAY DIFFRACTION2A71 - 179
3X-RAY DIFFRACTION3A180 - 265
4X-RAY DIFFRACTION4A266 - 270

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