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- PDB-6lhe: Crystal Structure of Gold-bound NDM-1 -

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Basic information

Entry
Database: PDB / ID: 6lhe
TitleCrystal Structure of Gold-bound NDM-1
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / GOLD
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
: / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.206 Å
AuthorsWang, H. / Sun, H. / Wang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)17307017 Hong Kong
CitationJournal: Nat Commun / Year: 2020
Title: Resensitizing carbapenem- and colistin-resistant bacteria to antibiotics using auranofin.
Authors: Sun, H. / Zhang, Q. / Wang, R. / Wang, H. / Wong, Y.T. / Wang, M. / Hao, Q. / Yan, A. / Kao, R.Y. / Ho, P.L. / Li, H.
History
DepositionDec 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 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
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,63810
Polymers51,2642
Non-polymers1,3748
Water7,512417
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4156
Polymers25,6321
Non-polymers7835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2234
Polymers25,6321
Non-polymers5913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.470, 73.760, 77.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 25631.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C7C422, beta-lactamase
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG3350 20%, 0.1M ammonium sulfate, 0.1M MES pH 6.0
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2019 / Details: NULL
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.206→70.47 Å / Num. obs: 239737 / % possible obs: 99.6 % / Redundancy: 12.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.018 / Rrim(I) all: 0.061 / Net I/σ(I): 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.21-1.249.90.7129023990870.8260.2370.7533.299.3
5.39-70.479.10.0581361614890.9740.0230.06341.395.3

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.14_3260:000refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZGE

5zge


Resolution: 1.206→50.953 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 20.27
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.1896 12861 5.36 %
Rwork0.1748 --
obs0.1756 239737 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.15 Å2 / Biso mean: 20.3099 Å2 / Biso min: 10.05 Å2
Refinement stepCycle: final / Resolution: 1.206→50.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 16 417 3746
Biso mean--24.12 32.4 -
Num. residues----449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.206-1.21920.28054150.2779755999
1.2192-1.23360.2924040.2756752498
1.2336-1.24860.25653970.2452734896
1.2486-1.26440.23594330.2334737397
1.2644-1.28110.22393940.2157630100
1.2811-1.29860.22054420.20957554100
1.2986-1.31720.21434620.20817583100
1.3172-1.33680.22593950.20397624100
1.3368-1.35770.22054180.20377597100
1.3577-1.380.22713930.19937661100
1.38-1.40380.21043720.1987583100
1.4038-1.42930.23453960.19627642100
1.4293-1.45680.21834020.18937694100
1.4568-1.48650.18964770.1857519100
1.4865-1.51890.19284180.18627598100
1.5189-1.55420.20664480.1847757999
1.5542-1.59310.19233880.17917645100
1.5931-1.63610.18273710.18337681100
1.6361-1.68430.19884320.17817606100
1.6843-1.73870.17694960.1737526100
1.7387-1.80080.19474610.1744754399
1.8008-1.87290.18434710.17347574100
1.8729-1.95810.17314060.16947657100
1.9581-2.06140.20264290.15867625100
2.0614-2.19050.17794410.16377551100
2.1905-2.35970.17774090.16057634100
2.3597-2.59710.18785070.16737547100
2.5971-2.97290.17934620.16957562100
2.9729-3.74540.17025150.158747499
3.7454-50.9530.19644070.1791718394
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)
10.0267-0.0301-0.02230.05370.0070.04530.06070.06320.1132-0.0442-0.05-0.0334-0.208-0.0187-0.00010.205-0.0037-0.01190.19870.02340.177715.379314.1545-21.6567
20.1297-0.06730.05580.21450.0670.2431-0.05430.01780.01950.0064-0.00420.0033-0.08130.024100.1265-0.0014-0.01670.13680.00340.133714.05958.5485-14.4085
30.1572-0.0730.02350.3645-0.12750.3589-0.00340.0194-0.00080.0049-0.0095-0.02040.02140.016100.11920.0055-0.00570.14410.00270.11615.9228-6.4586-17.3482
40.09510.10140.0310.11010.03250.0244-0.08220.0004-0.0178-0.14660.01290.00760.16230.1134-0.00770.18790.03880.03480.20310.01710.1323.6556-11.6156-31.9746
50.1920.0172-0.25320.03660.04370.45960.1705-0.04460.0141-0.04080.09850.0699-0.16550.17070.02450.18730.0074-0.04460.1315-0.00640.189918.3305-48.5208-1.302
60.1306-0.06780.09270.2029-0.03330.19750.06320.0236-0.0465-0.0830.030.17410.07360.0590.00420.157-0.0023-0.04510.1179-0.00540.219113.4471-43.0064-6.3428
70.2446-0.19890.20060.7567-0.10460.16060.0467-0.0133-0.0378-0.07460.00290.08690.03180.04020.00920.1329-0.0011-0.02770.13350.00170.146318.0535-28.2391-5.9284
80.0195-0.00510.02150.0012-0.00570.0235-0.04650.11580.0678-0.05780.0442-0.0010.0481-0.0791-0.00010.12730.0124-0.02730.15050.00970.168733.6371-24.33571.2442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 57 )A42 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 118 )A58 - 118
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 255 )A119 - 255
4X-RAY DIFFRACTION4chain 'A' and (resid 256 through 270 )A256 - 270
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 57 )B43 - 57
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 118 )B58 - 118
7X-RAY DIFFRACTION7chain 'B' and (resid 119 through 255 )B119 - 255
8X-RAY DIFFRACTION8chain 'B' and (resid 256 through 270 )B256 - 270

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