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- PDB-6zyq: Structure of NDM-1 with 2-Mercaptomethyl-thiazolidine D-syn-1b -

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Basic information

Entry
Database: PDB / ID: 6zyq
TitleStructure of NDM-1 with 2-Mercaptomethyl-thiazolidine D-syn-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-QST / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)52,56410
Polymers51,5522
Non-polymers1,0138
Water5,296294
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)26,1864
Polymers25,7761
Non-polymers4103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.180, 73.840, 77.440
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 116 or resid 118 through 270))
21(chain B and (resid 43 through 116 or resid 118 through 270))

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
11ASPASPALAALA(chain A and (resid 43 through 116 or resid 118 through 270))AA43 - 11617 - 90
12VALVALARGARG(chain A and (resid 43 through 116 or resid 118 through 270))AA118 - 27092 - 244
21ASPASPALAALA(chain B and (resid 43 through 116 or resid 118 through 270))BB43 - 11617 - 90
22VALVALARGARG(chain B and (resid 43 through 116 or resid 118 through 270))BB118 - 27092 - 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 BL21(DE3) (bacteria) / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-QST / (2~{S},4~{S})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid


Mass: 279.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17NO4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 1.95 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1M bis-tris pH 5.8, 32% PEG 3350, 0.15M NH4SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 1.7→38.72 Å / Num. obs: 44786 / % possible obs: 99.5 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.74 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3076 / CC1/2: 0.473 / Rpim(I) all: 0.596

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Processing

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

6rmf


Resolution: 1.7→38.72 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 2151 4.81 %
Rwork0.1775 42570 -
obs0.1785 44721 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.7 Å2 / Biso mean: 32.8182 Å2 / Biso min: 14.31 Å2
Refinement stepCycle: final / Resolution: 1.7→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3485 0 64 294 3843
Biso mean--40.37 40.33 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093624
X-RAY DIFFRACTIONf_angle_d0.9884946
X-RAY DIFFRACTIONf_chiral_restr0.075550
X-RAY DIFFRACTIONf_plane_restr0.006651
X-RAY DIFFRACTIONf_dihedral_angle_d14.8771256
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2052X-RAY DIFFRACTION7.744TORSIONAL
12B2052X-RAY DIFFRACTION7.744TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.73950.35221360.3064259593
1.7395-1.7830.28961350.2748281799
1.783-1.83130.2861230.24382829100
1.8313-1.88510.25351440.20772834100
1.8851-1.9460.21611510.19222812100
1.946-2.01550.21831400.18172804100
2.0155-2.09620.1981480.17662837100
2.0962-2.19160.19771290.16922830100
2.1916-2.30720.20281420.16862832100
2.3072-2.45170.22981080.16832890100
2.4517-2.64090.17181810.1662808100
2.6409-2.90660.18291300.16992888100
2.9066-3.3270.16911950.16792820100
3.327-4.19090.20021570.15622908100
4.1909-38.720.18581320.18283066100
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)
11.59520.53630.2021.1093-0.01650.0339-0.0419-0.49560.00560.3610.1266-0.7402-0.0780.7098-0.09670.74280.0247-0.08070.8181-0.00730.726225.8578-11.728526.1738
23.2894-1.0251-1.51093.89651.50854.82950.0089-0.0079-0.05550.22750.0379-0.21880.34130.2639-0.05020.2308-0.00960.00810.20140.05280.186515.3155-13.692621.1358
34.7559-0.7859-0.79782.3456-0.10423.21880.1434-0.08120.25450.0292-0.0825-0.4891-0.0550.649-0.0630.18570.00030.00440.28080.00060.254224.8099-7.389418.0699
40.7990.1084-0.33921.95560.19190.9534-0.02720.02290.0124-0.12980.040.0054-0.01990.0206-0.01150.1487-0.0142-0.00160.18910.01070.147813.30680.912613.1563
51.2749-0.74690.26642.0537-2.24763.2136-0.09960.14940.1535-0.0314-0.1148-0.3990.08540.44460.23670.2929-0.0387-0.01570.3720.01750.260328.032910.830523.8532
60.7984-0.18710.05712.2522-0.16481.9739-0.0061-0.0807-0.04890.28360.0373-0.017-0.09450.1468-0.04370.20180-0.00620.21640.00270.140118.60198.331129.2822
70.5701-0.563-1.46062.99892.03455.38240.38730.19520.2704-0.46360.0931-0.2124-0.30810.3004-0.39270.3938-0.03520.06280.2374-0.02630.329618.462748.5231.8775
82.73290.2171-0.51593.05520.54532.5977-0.0153-0.24330.02810.13820.0283-0.5112-0.08370.54280.01660.3141-0.01820.06210.2968-0.0230.48124.843142.4559.4632
91.282-0.1056-0.13392.555-0.0771.60860.05180.20390.1549-0.1971-0.06140.2829-0.18690.04790.00920.2277-0.0007-0.03460.1776-0.01430.302312.157942.7276.6392
101.13340.2217-0.41532.83550.06370.76920.09150.08580.0415-0.0548-0.06060.2061-0.020.0164-0.03970.23240.01210.02880.171-0.00190.213613.280728.28458.1764
111.32990.9926-0.08492.8767-1.17612.22050.3275-0.2681-0.1510.5713-0.3621-0.7186-0.23050.29780.03650.3819-0.10150.01020.413-0.07250.498831.978726.33866.9558
121.84850.4453-0.36912.36260.27451.48520.03230.0329-0.0751-0.23640.019-0.157-0.04870.2353-0.03110.2889-0.0460.06010.2889-0.00940.318727.840927.0612-1.9201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 43 )A31 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 57 )A44 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 70 )A58 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 212 )A71 - 212
5X-RAY DIFFRACTION5chain 'A' and (resid 213 through 228 )A213 - 228
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 270 )A229 - 270
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 57 )B43 - 57
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 70 )B58 - 70
9X-RAY DIFFRACTION9chain 'B' and (resid 71 through 118 )B71 - 118
10X-RAY DIFFRACTION10chain 'B' and (resid 119 through 209 )B119 - 209
11X-RAY DIFFRACTION11chain 'B' and (resid 210 through 228 )B210 - 228
12X-RAY DIFFRACTION12chain 'B' and (resid 229 through 270 )B229 - 270

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