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

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Basic information

Entry
Database: PDB / ID: 8gpc
TitleCrystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed ampicillin
ComponentsMetallo beta lactamase NDM-1
KeywordsHYDROLASE
Function / homologyMetallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / beta-lactamase activity / beta-lactamase / Chem-ZZ7 / Metallo-beta-lactamase type 2
Function and homology information
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

Downloads & links

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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)58,0749
Polymers57,0552
Non-polymers1,0197
Water10,791599
1
A: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0495
Polymers28,5271
Non-polymers5214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area10020 Å2
MethodPISA
2
B: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0264
Polymers28,5271
Non-polymers4983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.260, 79.110, 134.350
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 / 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-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 367.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 1.83 Å3/Da / Density % sol: 32.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Succinate pH5.5, 28%PEG3350 / PH range: 5.4-5.6

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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→33.59 Å / Num. obs: 81150 / % possible obs: 97.4 % / Redundancy: 7.9 % / Biso Wilson estimate: 13.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.51
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 16271 / CC1/2: 0.858

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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→33.59 Å / SU ML: 0.1086 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 14.0768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1603 4139 5.1 %
Rwork0.13 77011 -
obs0.1315 81150 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.26 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 55 599 4230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093748
X-RAY DIFFRACTIONf_angle_d1.1765120
X-RAY DIFFRACTIONf_chiral_restr0.0958574
X-RAY DIFFRACTIONf_plane_restr0.011689
X-RAY DIFFRACTIONf_dihedral_angle_d6.3274554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.23711180.18391918X-RAY DIFFRACTION75.16
1.42-1.430.23791120.14732089X-RAY DIFFRACTION80.77
1.43-1.450.14911260.12632263X-RAY DIFFRACTION86.12
1.45-1.470.17521270.12012382X-RAY DIFFRACTION91.54
1.47-1.490.17121210.12122472X-RAY DIFFRACTION95.12
1.49-1.510.17011380.12212468X-RAY DIFFRACTION94.63
1.51-1.530.20081420.11422569X-RAY DIFFRACTION98.91
1.53-1.550.16741440.11422596X-RAY DIFFRACTION99.6
1.55-1.580.17061380.11342635X-RAY DIFFRACTION99.82
1.58-1.60.16851310.11252575X-RAY DIFFRACTION99.96
1.6-1.630.17691410.11042623X-RAY DIFFRACTION99.93
1.63-1.660.16531560.10842586X-RAY DIFFRACTION99.93
1.66-1.690.17591560.10652610X-RAY DIFFRACTION99.93
1.69-1.730.14861370.10692608X-RAY DIFFRACTION99.96
1.73-1.760.15221360.10812624X-RAY DIFFRACTION99.93
1.76-1.80.17221540.11632601X-RAY DIFFRACTION99.93
1.8-1.850.16291300.11942618X-RAY DIFFRACTION99.82
1.85-1.90.16861450.12352613X-RAY DIFFRACTION99.89
1.9-1.960.14671470.11352654X-RAY DIFFRACTION99.93
1.96-2.020.13721450.1192591X-RAY DIFFRACTION99.93
2.02-2.090.15831410.12322645X-RAY DIFFRACTION99.93
2.09-2.170.17491180.12612669X-RAY DIFFRACTION99.82
2.17-2.270.15871400.12542636X-RAY DIFFRACTION100
2.27-2.390.18721370.13342649X-RAY DIFFRACTION99.96
2.39-2.540.15541420.13662655X-RAY DIFFRACTION99.82
2.54-2.740.15451520.14262665X-RAY DIFFRACTION99.93
2.74-3.020.1641200.14232715X-RAY DIFFRACTION99.89
3.02-3.450.15271480.14082682X-RAY DIFFRACTION99.96
3.45-4.350.13451410.13352747X-RAY DIFFRACTION99.79
4.35-33.590.16671560.14442853X-RAY DIFFRACTION99.64

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