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

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Basic information

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


antibiotic catabolic process / beta-lactamase activity / periplasmic space / response to antibiotic / 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-PNK / BlaNDM1
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)58,0609
Polymers57,0552
Non-polymers1,0067
Water11,602644
1
A: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0505
Polymers28,5271
Non-polymers5224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0114
Polymers28,5271
Non-polymers4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.170, 79.160, 134.120
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) / Strain (production host): BL21(DE3) / 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-PNK / (2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / Penicillin, hydroxylated form


Mass: 352.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O5S / Comment: antibiotic*YM
#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.: 644 / 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: 32.5 %
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→38.93 Å / Num. obs: 81080 / % possible obs: 97.6 % / Redundancy: 9.4 % / Biso Wilson estimate: 11.11 Å2 / CC1/2: 0.998 / Net I/σ(I): 18.47
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 16723 / CC1/2: 0.869

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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→38.93 Å / SU ML: 0.1107 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 13.7358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1598 4137 5.1 %
Rwork0.1295 76938 -
obs0.131 81075 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.62 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 53 644 4273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693770
X-RAY DIFFRACTIONf_angle_d0.99145153
X-RAY DIFFRACTIONf_chiral_restr0.0888577
X-RAY DIFFRACTIONf_plane_restr0.0089693
X-RAY DIFFRACTIONf_dihedral_angle_d6.0861563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.24771100.18341951X-RAY DIFFRACTION76.19
1.42-1.430.227980.1492116X-RAY DIFFRACTION81.7
1.43-1.450.1971320.11972317X-RAY DIFFRACTION88.25
1.45-1.470.16381160.10992344X-RAY DIFFRACTION91.18
1.47-1.490.15091410.10452457X-RAY DIFFRACTION94.85
1.49-1.510.17351360.1072559X-RAY DIFFRACTION97.82
1.51-1.530.15331420.10132545X-RAY DIFFRACTION99.15
1.53-1.550.14631230.10312625X-RAY DIFFRACTION99.17
1.55-1.580.16831340.10392587X-RAY DIFFRACTION99.56
1.58-1.60.17031340.10732577X-RAY DIFFRACTION99.96
1.6-1.630.15331380.11512630X-RAY DIFFRACTION100
1.63-1.660.1891500.12482590X-RAY DIFFRACTION100
1.66-1.690.15411410.11792593X-RAY DIFFRACTION99.96
1.69-1.730.15461500.11592601X-RAY DIFFRACTION99.89
1.73-1.760.17061350.11642618X-RAY DIFFRACTION100
1.76-1.80.15971480.11372597X-RAY DIFFRACTION99.96
1.8-1.850.15991280.11372619X-RAY DIFFRACTION99.96
1.85-1.90.15931330.1192604X-RAY DIFFRACTION100
1.9-1.960.15181430.1222660X-RAY DIFFRACTION99.96
1.96-2.020.15041300.12712602X-RAY DIFFRACTION100
2.02-2.090.15031650.12742610X-RAY DIFFRACTION99.93
2.09-2.170.1581360.12282645X-RAY DIFFRACTION99.89
2.17-2.270.15371520.12182618X-RAY DIFFRACTION100
2.27-2.390.15931660.12952605X-RAY DIFFRACTION99.96
2.39-2.540.14781340.13412660X-RAY DIFFRACTION99.89
2.54-2.740.14681400.14142660X-RAY DIFFRACTION99.93
2.74-3.020.17491530.13982679X-RAY DIFFRACTION99.96
3.02-3.450.15891460.13982667X-RAY DIFFRACTION99.93
3.45-4.350.141460.13392729X-RAY DIFFRACTION99.65
4.35-38.930.17781370.15472873X-RAY DIFFRACTION99.77

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