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- PDB-5xp6: native structure of NDM-1 crystallized at pH5.5 -

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Basic information

Entry
Database: PDB / ID: 5xp6
Titlenative structure of NDM-1 crystallized at pH5.5
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / antibiotic resistant / metallo-beta-lactamase / native structure
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
HYDROXIDE ION / SUCCINIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.95 Å
AuthorsZhang, H. / Ma, G. / Lai, J. / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,29510
Polymers25,7191
Non-polymers5769
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-51 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.425, 59.807, 42.098
Angle α, β, γ (deg.)90.000, 97.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: C7C422, beta-lactamase

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Non-polymers , 5 types, 339 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Succinic acid at pH 5.5, 15%(w/v) PEG3350 and 20mM L-proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 0.95→50 Å / Num. obs: 127274 / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.094 / Χ2: 1.044 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
0.95-0.983.50.1981.043196.3
0.98-1.024.70.1890.9291100
1.02-1.077.60.2050.8981100
1.07-1.137.60.1520.9611100
1.13-1.27.70.131.131100
1.2-1.297.90.1221.0521100
1.29-1.4280.1191.0051100
1.42-1.6280.1111.1411100
1.62-2.057.90.0931.1331100
2.05-506.40.081.092199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6X

3q6x
PDB Unreleased entry


Resolution: 0.95→41.71 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.349 / SU ML: 0.009 / SU R Cruickshank DPI: 0.0179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1367 6394 5 %RANDOM
Rwork0.1267 ---
obs0.1272 120850 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 44.29 Å2 / Biso mean: 8.969 Å2 / Biso min: 4 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 0.95→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 31 330 2062
Biso mean--13.04 19.62 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021887
X-RAY DIFFRACTIONr_bond_other_d0.0020.021256
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9412579
X-RAY DIFFRACTIONr_angle_other_deg0.8383.0013087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90424.76284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50115299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.986159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02380
X-RAY DIFFRACTIONr_rigid_bond_restr1.15933143
X-RAY DIFFRACTIONr_sphericity_free12.479555
X-RAY DIFFRACTIONr_sphericity_bonded5.32553368
LS refinement shellResolution: 0.95→0.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 432 -
Rwork0.177 8589 -
all-9021 -
obs--97.06 %

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