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- PDB-8gpd: Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with h... -

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Basic information

Entry
Database: PDB / ID: 8gpd
TitleCrystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed penicillin V
ComponentsMetallo beta lactamase NDM-1
KeywordsHYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-JXF / : / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsShi, X. / Dai, Y. / Zhang, Q. / Liu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Interplay between the beta-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design.
Authors: Shi, X. / Dai, Y. / Lan, Z. / Wang, S. / Cui, L. / Xiao, C. / Zhao, K. / Li, X. / Liu, W. / Zhang, Q.
History
DepositionAug 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo beta lactamase NDM-1
B: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0929
Polymers57,0552
Non-polymers1,0387
Water11,494638
1
A: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0274
Polymers28,5271
Non-polymers4993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0665
Polymers28,5271
Non-polymers5384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.140, 79.050, 134.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Metallo beta lactamase NDM-1 / Metallo beta-lactamase / Metallo-beta-lactamase NDM1 / Metallobetalactamase NDM-1 / NDM-1 / NDM1 ...Metallo beta-lactamase / Metallo-beta-lactamase NDM1 / Metallobetalactamase NDM-1 / NDM-1 / NDM1 metallo-beta-lactamase / New Delhi Metallo carbapenemase-1 / New Delhi metallo-beta-lactamase NDM-1 / New Delhi metallo-beta-lactamse 1


Mass: 28527.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1, bla NDM-1, blaNDM1, NDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9NWK5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-JXF / (2R,4S)-5,5-dimethyl-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-phenoxyethanoylamino)ethyl]-1,3-thiazolidine-4-carboxylic acid


Mass: 368.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.82 Å3/Da / Density % sol: 32.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Succinate pH5.5, 32%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.4→35.08 Å / Num. obs: 79892 / % possible obs: 96.2 % / Redundancy: 10.2 % / Biso Wilson estimate: 11.58 Å2 / CC1/2: 0.997 / Net I/σ(I): 16.32
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 17119 / CC1/2: 0.897

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIX1.19.1_4122phasing
PHENIX1.19.1_4122refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RL2

4rl2


Resolution: 1.4→35.08 Å / SU ML: 0.1034 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 13.7895
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1599 4081 5.11 %
Rwork0.124 75797 -
obs0.1258 79878 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.58 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 55 638 4269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863811
X-RAY DIFFRACTIONf_angle_d1.13135213
X-RAY DIFFRACTIONf_chiral_restr0.0945582
X-RAY DIFFRACTIONf_plane_restr0.0092702
X-RAY DIFFRACTIONf_dihedral_angle_d6.1973576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.21241030.16461903X-RAY DIFFRACTION71.75
1.42-1.430.17271040.13282053X-RAY DIFFRACTION76.98
1.43-1.450.18541170.11552165X-RAY DIFFRACTION79.79
1.45-1.470.17991230.1122265X-RAY DIFFRACTION85.56
1.47-1.490.16371350.10452373X-RAY DIFFRACTION88.31
1.49-1.510.16281110.10182526X-RAY DIFFRACTION93.31
1.51-1.540.17291320.09432606X-RAY DIFFRACTION98.17
1.54-1.560.15371490.09572696X-RAY DIFFRACTION99.3
1.56-1.580.14591390.09822686X-RAY DIFFRACTION99.86
1.58-1.610.14711420.0992697X-RAY DIFFRACTION99.72
1.61-1.640.16171460.10362687X-RAY DIFFRACTION99.82
1.64-1.670.14911490.10492650X-RAY DIFFRACTION99.86
1.67-1.710.16661690.10622698X-RAY DIFFRACTION99.9
1.71-1.740.17371230.11542699X-RAY DIFFRACTION99.86
1.74-1.780.15021320.10852711X-RAY DIFFRACTION99.68
1.78-1.830.16111470.1122674X-RAY DIFFRACTION99.89
1.83-1.880.13391580.11242719X-RAY DIFFRACTION99.93
1.88-1.930.16791470.1162671X-RAY DIFFRACTION99.82
1.93-20.15571320.12032728X-RAY DIFFRACTION99.93
2-2.070.17251400.12322719X-RAY DIFFRACTION99.83
2.07-2.150.16851570.12312710X-RAY DIFFRACTION99.83
2.15-2.250.13281490.11692698X-RAY DIFFRACTION99.93
2.25-2.370.15571390.12412733X-RAY DIFFRACTION99.97
2.37-2.520.16241670.13162725X-RAY DIFFRACTION99.97
2.52-2.710.17461560.14222727X-RAY DIFFRACTION99.76
2.71-2.980.18071310.13952777X-RAY DIFFRACTION99.73
2.98-3.410.16711490.13592780X-RAY DIFFRACTION100
3.41-4.30.14471490.12362812X-RAY DIFFRACTION99.8
4.3-35.080.15621860.14282909X-RAY DIFFRACTION99.14

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