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- PDB-6zyp: Structure of NDM-1 with 2-Mercaptomethyl-thiazolidine L-anti-1b -

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Basic information

Entry
Database: PDB / ID: 6zyp
TitleStructure of NDM-1 with 2-Mercaptomethyl-thiazolidine L-anti-1b
ComponentsMetallo-beta-lactamase type 2
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance / lactamase / zinc / inhibitor
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
Chem-QT2 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI100560 United States
CitationJournal: Chem Sci / Year: 2021
Title: 2-Mercaptomethyl-thiazolidines use conserved aromatic-S interactions to achieve broad-range inhibition of metallo-beta-lactamases.
Authors: Rossi, M.A. / Martinez, V. / Hinchliffe, P. / Mojica, M.F. / Castillo, V. / Moreno, D.M. / Smith, R. / Spellberg, B. / Drusano, G.L. / Banchio, C. / Bonomo, R.A. / Spencer, J. / Vila, A.J. / Mahler, G.
History
DepositionAug 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2859
Polymers51,5522
Non-polymers7337
Water8,737485
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3786
Polymers25,7761
Non-polymers6025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9073
Polymers25,7761
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.974, 74.178, 77.956
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 43 through 44 or resid 46...
21(chain B and (resid 43 through 44 or resid 46...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLNGLN(chain A and (resid 43 through 44 or resid 46...AA43 - 4417 - 18
12PHEPHEMETMET(chain A and (resid 43 through 44 or resid 46...AA46 - 6720 - 41
13GLYGLYALAALA(chain A and (resid 43 through 44 or resid 46...AA69 - 11643 - 90
14VALVALGLYGLY(chain A and (resid 43 through 44 or resid 46...AA118 - 12892 - 102
15ASPASPLEULEU(chain A and (resid 43 through 44 or resid 46...AA130 - 180104 - 154
16VALVALALAALA(chain A and (resid 43 through 44 or resid 46...AA182 - 215156 - 189
17SERSERALAALA(chain A and (resid 43 through 44 or resid 46...AA217 - 263191 - 237
18METMETARGARG(chain A and (resid 43 through 44 or resid 46...AA265 - 270239 - 244
21ASPASPGLNGLN(chain B and (resid 43 through 44 or resid 46...BB43 - 4417 - 18
22PHEPHEMETMET(chain B and (resid 43 through 44 or resid 46...BB46 - 6720 - 41
23GLYGLYALAALA(chain B and (resid 43 through 44 or resid 46...BB69 - 11643 - 90
24VALVALGLYGLY(chain B and (resid 43 through 44 or resid 46...BB118 - 12892 - 102
25ASPASPARGARG(chain B and (resid 43 through 44 or resid 46...BB43 - 27017 - 244
26VALVALALAALA(chain B and (resid 43 through 44 or resid 46...BB182 - 215156 - 189
27METMETARGARG(chain B and (resid 43 through 44 or resid 46...BB265 - 270239 - 244

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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: 25775.951 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 (E. coli) / References: UniProt: C7C422, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-QT2 / (2~{S},4~{R})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid


Mass: 279.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17NO4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 485 / 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: 1.96 Å3/Da / Density % sol: 37.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1M bis-tris pH 5.8, 32% PEG 3350, 0.15M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97634 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97634 Å / Relative weight: 1
ReflectionResolution: 1.4→53.74 Å / Num. obs: 79630 / % possible obs: 99 % / Redundancy: 12.3 % / CC1/2: 0.997 / Rpim(I) all: 0.039 / Net I/σ(I): 11.1
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3694 / CC1/2: 0.584 / Rpim(I) all: 0.344

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RMF

6rmf


Resolution: 1.4→42.62 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 16.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1873 4225 5.31 %
Rwork0.1635 75334 -
obs0.1649 79559 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.53 Å2 / Biso mean: 21.5613 Å2 / Biso min: 5.14 Å2
Refinement stepCycle: final / Resolution: 1.4→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 47 485 4026
Biso mean--23.51 29.95 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083625
X-RAY DIFFRACTIONf_angle_d1.0074945
X-RAY DIFFRACTIONf_chiral_restr0.084550
X-RAY DIFFRACTIONf_plane_restr0.007653
X-RAY DIFFRACTIONf_dihedral_angle_d15.7231262
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2420X-RAY DIFFRACTION5.519TORSIONAL
12B2420X-RAY DIFFRACTION5.519TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.41590.25041140.2586237094
1.4159-1.43260.27151420.2377235395
1.4326-1.450.25711350.2275239896
1.45-1.46840.22111420.2132244397
1.4684-1.48770.22631690.2117243898
1.4877-1.50810.20141390.1947245999
1.5081-1.52970.23791250.1891251699
1.5297-1.55250.18691440.1792248398
1.5525-1.57670.21241480.1772246599
1.5767-1.60260.20481610.168246199
1.6026-1.63020.17171360.1642252199
1.6302-1.65990.20861180.1626251699
1.6599-1.69180.1991280.1572249699
1.6918-1.72630.1893930.1561255899
1.7263-1.76390.17711180.15512541100
1.7639-1.80490.1621050.15712541100
1.8049-1.850.16921090.15372533100
1.85-1.90010.17711400.1502252699
1.9001-1.9560.17941290.14852527100
1.956-2.01910.17411370.14242526100
2.0191-2.09130.16921390.14342529100
2.0913-2.1750.15521550.1419252799
2.175-2.2740.20651730.13722499100
2.274-2.39390.14661510.14282546100
2.3939-2.54380.16791630.1512524100
2.5438-2.74020.18071980.15682527100
2.7402-3.01590.17561480.16542556100
3.0159-3.45210.19071340.16062607100
3.4521-4.34870.1781670.15722613100
4.3487-42.620.21331650.19142735100
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)
13.3888-2.4161-1.92452.56231.49741.39450.22190.2478-0.195-0.4118-0.12480.42290.4072-0.0038-0.06110.28450.0032-0.1170.4382-0.04450.3535-26.4105-12.0666-26.2726
22.18382.3327-3.11565.2727-2.22656.9179-0.13730.1573-0.2098-0.23930.07910.08090.5495-0.10860.00960.14020.01920.01210.0774-0.0180.0849-15.295-13.9456-21.5349
33.2037-0.6351-0.11732.7420.08962.26880.0273-0.11560.02030.04640.03110.40690.0585-0.43910.06130.0956-0.01020.02240.15020.00260.1134-24.7795-7.6369-18.5509
40.399-0.0132-0.23551.66320.00720.592-0.022-0.0424-0.00820.07620.0299-0.03010.02740.0302-0.00380.06210.0149-0.00350.0847-0.00780.0496-13.43280.6408-11.6952
54.3519-0.89251.54884.0273-0.1582.10170.12050.1033-0.0473-0.1507-0.0069-0.03520.00930.0135-0.01130.0910.00490.00930.0816-0.01340.0324-13.21222.7843-24.706
63.42230.11450.49914.75362.01675.2133-0.069-0.04360.07140.1834-0.11910.58910.0672-0.41510.19220.09490.03840.01370.18320.00230.126-28.04810.9237-24.4026
71.04250.58710.19663.5168-0.17612.5157-0.00370.0156-0.0148-0.27250.00660.0637-0.1358-0.08180.00120.1040.0134-0.01330.0943-0.00930.0308-18.54758.3324-29.5831
81.62190.6999-1.08965.0692-3.04432.54050.1407-0.20590.21680.50040.14860.1435-0.4915-0.1504-0.23280.22480.01240.04990.1122-0.00590.1695-18.43248.7585-1.9717
95.11040.24261.69312.95670.15544.91130.01470.37770.1877-0.2656-0.04340.4983-0.0686-0.43650.07270.13750.0208-0.03020.14830.01160.2201-24.798742.5381-9.5293
102.8409-0.07390.15673.19250.04993.1819-0.0268-0.15950.16190.11530.0052-0.0381-0.0343-0.0749-0.04570.08330.00620.0070.06050.00870.1277-14.926940.1311-5.6451
112.93160.1791.28844.77440.81332.8235-0.0780.02720.15690.12740.0469-0.3889-0.25780.02920.05570.0874-0.00390.02540.09560.01880.1498-9.844845.3199-7.9162
121.0758-0.0148-0.41962.8147-0.5041.15420.04540.02670.1015-0.1631-0.0343-0.0825-0.00540.0424-0.00940.0844-0.00210.01970.084-0.00640.1181-12.652127.7579-10.3688
135.4470.39-0.39022.81220.83532.00590.0553-0.1992-0.01820.07450.08040.0337-0.0848-0.0018-0.11570.13920.01010.03330.09840.01990.1001-22.452332.26911.4458
141.6666-0.3951-0.00353.04070.79271.87390.01590.03330.00060.0384-0.03190.221-0.0427-0.1295-0.00110.0910.00570.03060.15770.01970.1569-26.884427.1238-1.5579
156.26252.23972.9263.22981.48097.20180.06660.0737-0.1650.03630.06420.22320.151-0.228-0.03160.09390.01340.03140.14390.00770.1795-33.586123.86780.8052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 42 )A30 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 57 )A43 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 70 )A58 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 194 )A71 - 194
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 212 )A195 - 212
6X-RAY DIFFRACTION6chain 'A' and (resid 213 through 228 )A213 - 228
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 270 )A229 - 270
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 57 )B43 - 57
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 70 )B58 - 70
10X-RAY DIFFRACTION10chain 'B' and (resid 71 through 94 )B71 - 94
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 118 )B95 - 118
12X-RAY DIFFRACTION12chain 'B' and (resid 119 through 194 )B119 - 194
13X-RAY DIFFRACTION13chain 'B' and (resid 195 through 215 )B195 - 215
14X-RAY DIFFRACTION14chain 'B' and (resid 216 through 255 )B216 - 255
15X-RAY DIFFRACTION15chain 'B' and (resid 256 through 270 )B256 - 270

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