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- PDB-6zyr: Structure of IMP-1 with 2-Mercaptomethyl-thiazolidine L-anti-1b -

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Basic information

Entry
Database: PDB / ID: 6zyr
TitleStructure of IMP-1 with 2-Mercaptomethyl-thiazolidine L-anti-1b
ComponentsBeta-lactamase IMP-1
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
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
ACETATE ION / Chem-QT2 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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: Beta-lactamase IMP-1
B: Beta-lactamase IMP-1
C: Beta-lactamase IMP-1
D: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,23723
Polymers101,2034
Non-polymers2,03319
Water9,908550
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A: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7735
Polymers25,3011
Non-polymers4724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9829
Polymers25,3011
Non-polymers6818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7705
Polymers25,3011
Non-polymers4694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7114
Polymers25,3011
Non-polymers4103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.555, 78.003, 261.107
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 3 through 60 or resid 62...
21(chain B and (resid 3 through 60 or resid 62...
31(chain C and (resid 3 through 60 or resid 62...
41(chain D and (resid 3 through 60 or resid 62...

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
11SERSERVALVAL(chain A and (resid 3 through 60 or resid 62...AA3 - 605 - 62
12TRPTRPVALVAL(chain A and (resid 3 through 60 or resid 62...AA62 - 6464 - 66
13ARGARGGLYGLY(chain A and (resid 3 through 60 or resid 62...AA66 - 16668 - 168
14LEULEULYSLYS(chain A and (resid 3 through 60 or resid 62...AA168 - 221170 - 223
21SERSERVALVAL(chain B and (resid 3 through 60 or resid 62...BB3 - 605 - 62
22TRPTRPVALVAL(chain B and (resid 3 through 60 or resid 62...BB62 - 6464 - 66
23ARGARGGLYGLY(chain B and (resid 3 through 60 or resid 62...BB66 - 16668 - 168
24LEULEULYSLYS(chain B and (resid 3 through 60 or resid 62...BB168 - 221170 - 223
31SERSERVALVAL(chain C and (resid 3 through 60 or resid 62...CC3 - 605 - 62
32TRPTRPVALVAL(chain C and (resid 3 through 60 or resid 62...CC62 - 6464 - 66
33ARGARGGLYGLY(chain C and (resid 3 through 60 or resid 62...CC66 - 16668 - 168
34LEULEULYSLYS(chain C and (resid 3 through 60 or resid 62...CC168 - 221170 - 223
41SERSERVALVAL(chain D and (resid 3 through 60 or resid 62...DD3 - 605 - 62
42TRPTRPVALVAL(chain D and (resid 3 through 60 or resid 62...DD62 - 6464 - 66
43ARGARGGLYGLY(chain D and (resid 3 through 60 or resid 62...DD66 - 16668 - 168
44LEULEULYSLYS(chain D and (resid 3 through 60 or resid 62...DD168 - 221170 - 223

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase IMP-1 / BLAIMP / Beta-lactamase type II / Penicillinase / Class B1 Metallo-beta-lactamase IMP-1


Mass: 25300.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P52699, beta-lactamase

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Non-polymers , 6 types, 569 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / 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.: 4 / Source method: obtained synthetically / Formula: C10H17NO4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.0, 0.2 M sodium acetate, 25% PEG 8000. 1ul protein (25 mg/ml) mixed with 1ul reagent

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.87→66.962 Å / Num. obs: 83296 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.998 / Rpim(I) all: 0.053 / Net I/σ(I): 9.4
Reflection shellResolution: 1.87→1.91 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4472 / CC1/2: 0.542 / Rpim(I) all: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HH4

5hh4


Resolution: 1.87→66.962 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 4050 4.87 %
Rwork0.183 79109 -
obs0.1847 83159 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.64 Å2 / Biso mean: 41.3661 Å2 / Biso min: 14.21 Å2
Refinement stepCycle: final / Resolution: 1.87→66.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6870 0 182 550 7602
Biso mean--62.01 45.89 -
Num. residues----877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087176
X-RAY DIFFRACTIONf_angle_d0.8529748
X-RAY DIFFRACTIONf_chiral_restr0.0571080
X-RAY DIFFRACTIONf_plane_restr0.0051216
X-RAY DIFFRACTIONf_dihedral_angle_d18.732586
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4104X-RAY DIFFRACTION11.312TORSIONAL
12B4104X-RAY DIFFRACTION11.312TORSIONAL
13C4104X-RAY DIFFRACTION11.312TORSIONAL
14D4104X-RAY DIFFRACTION11.312TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.87-1.8920.34561420.36682623
1.892-1.91510.35521360.34282723
1.9151-1.93930.33771300.31262697
1.9393-1.96490.29011270.28942689
1.9649-1.99180.29431400.27962699
1.9918-2.02020.2891340.26642681
2.0202-2.05040.29441480.25662678
2.0504-2.08240.23551270.25192677
2.0824-2.11660.26741280.23662751
2.1166-2.15310.24881460.2242647
2.1531-2.19220.23621530.21922712
2.1922-2.23440.25361340.21312717
2.2344-2.280.25731430.19972655
2.28-2.32960.24371480.19862715
2.3296-2.38380.22771360.19342682
2.3838-2.44340.22211540.18432738
2.4434-2.50950.24651040.18432722
2.5095-2.58330.21961240.18622741
2.5833-2.66670.22151280.18542731
2.6667-2.7620.22661450.1912712
2.762-2.87260.25031380.19142770
2.8726-3.00330.2321550.17582707
3.0033-3.16170.18611380.17442736
3.1617-3.35970.2121490.16782750
3.3597-3.61910.21291320.15762760
3.6191-3.98330.19221680.14592764
3.9833-4.55960.17321360.13152813
4.5596-5.74410.18181470.14192829
5.7441-66.9620.18241600.15692990
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)
17.8676-2.7839-2.72885.1052.10887.7293-0.4585-0.80710.21311.02770.5506-0.2330.21360.3147-0.11140.49320.0265-0.0680.28980.05530.18364.984243.3459564.5691
24.729-0.0448-0.86243.21421.33793.1664-0.0796-0.38590.17720.32940.1149-0.3236-0.11320.3337-0.03890.27240.0001-0.0470.2070.00890.179367.0512245.5046555.1117
33.4972-1.1502-0.53275.68492.6224.5596-0.08350.08930.00190.0131-0.08970.2065-0.0402-0.1450.18440.2205-0.0267-0.02660.17330.05470.151658.6381243.9144544.6217
43.4450.1763-1.09943.4906-0.03593.9833-0.1051-0.3744-0.30270.43830.02120.0350.60870.05640.07710.38290.0060.02570.16670.03920.224759.507231.2355553.7808
52.5360.91210.01343.642-0.14774.1981-0.1908-0.4281-0.58520.84190.06710.3621.0747-0.2670.08360.6956-0.04660.13270.29940.1190.469255.8079224.7483559.7018
65.19454.043-1.7488.6006-2.84858.6162-0.43060.59670.2008-1.33430.21630.2274-0.2171-0.08680.15550.43450.0423-0.01930.2235-0.05010.192355.029247.0333510.0941
73.0232-2.9757-3.31346.05211.84515.46830.25650.35740.3115-1.0728-0.2908-0.45690.38550.3888-0.09170.48340.08370.13330.3080.02330.182964.952243.1872511.3894
84.0244-0.2598-0.33753.9833-1.65272.1295-0.03170.1416-0.098-0.4713-0.0290.13780.3776-0.08220.05210.18580.00410.00710.1861-0.03160.1456.6748244.1613518.695
94.4403-4.21680.64546.17750.32234.11820.20520.31550.3766-0.6432-0.0893-0.0212-0.07410.2205-0.0420.1585-0.0505-0.0070.21070.0330.191856.1176255.0718518.2171
104.9014-3.6421.68126.6548-1.64862.291-0.0252-0.04140.0066-0.3077-0.054-0.09970.28750.01640.0630.1339-0.02290.02740.2012-0.01660.146359.9928243.602523.8141
112.5235-0.764-0.30826.5798-0.27923.5857-0.0436-0.222-0.13020.00490.0269-0.26130.320.1517-0.02750.12990.03440.03530.20320.00080.148562.5942240.7578531.158
122.6093-0.9749-0.22084.81290.53433.1868-0.03920.3379-0.7491-0.7635-0.0360.10160.60380.01140.06480.4862-0.03630.06220.2168-0.08940.385359.3454227.2787516.5671
135.3486-2.29410.99585.8936-1.48315.840.29360.70760.6768-1.0439-0.101-0.5098-0.99980.1684-0.12980.5109-0.09810.05380.2258-0.00560.28652.3193280.0614543.4641
147.2779-0.89840.59552.8321-0.2128.1285-0.20560.1708-0.9077-0.22760.0365-0.26680.56040.68760.21740.3543-0.0390.11350.29020.01810.377254.5804269.7287543.9736
153.07150.7640.14515.9692-0.08022.35720.00240.0550.2697-0.1081-0.0167-0.3835-0.68390.3040.01090.3357-0.07040.00740.2043-0.00740.208755.4222278.252553.4476
162.28730.68591.17353.20290.97862.97760.0072-0.15330.14570.2286-0.0571-0.0193-0.3187-0.15990.03770.2314-0.00050.01150.2035-0.00870.14248.1881270.1983560.2499
175.8987-0.5488-0.46417.8071-1.45184.64960.0027-0.15240.19070.03180.07150.5022-0.2105-0.7574-0.1070.14020.0203-0.05690.3532-0.0650.140837.0158267.5201552.0707
183.52980.56240.58022.4488-0.43933.77580.15540.3508-0.4524-0.9467-0.26440.3670.5827-0.5990.08810.3153-0.0829-0.00690.4171-0.09280.279535.6842255.5502547.5249
193.4977-1.95441.8588.8483-1.17213.70990.08770.43610.0397-1.26490.14530.0319-0.3162-1.121-0.2680.49110.2549-0.02161.08510.0120.190844.6304237.7035576.1538
204.4267-2.09920.26464.7537-1.94815.79560.08890.3884-0.02970.0999-0.12010.1584-0.0782-1.0206-0.00460.36770.0444-0.03340.6564-0.00030.171144.6476233.1849583.6681
213.2528-0.18951.95572.8899-0.16754.73330.08710.5788-0.1571-0.2188-0.09570.5248-0.1767-1.2202-0.00110.36460.0781-0.01530.9212-0.02640.305538.922235.0802587.8761
222.40590.4292-1.41244.8833.07655.84440.3489-0.0409-0.01640.5905-0.3479-0.1161-0.0541-0.3009-0.02010.4931-0.0349-0.05410.58930.07790.22250.4006237.5406598.1043
234.6643.48030.47444.92643.00832.94470.3298-0.3655-0.47170.5301-0.5553-0.74830.36520.25580.21060.50290.0065-0.06020.53590.14080.280457.7136233.2348591.5616
244.1082.16441.3675.91564.60425.57220.5030.264-0.43660.4083-0.3574-0.35010.6539-0.0334-0.09850.42510.0731-0.10430.47120.08580.277755.7552227.8459584.0971
251.16821.5545-1.56637.28392.37056.3790.23750.1921-0.0533-0.278-0.1283-0.3494-0.28220.6537-0.11290.4010.0763-0.07650.66660.14890.263864.8699240.3924585.0824
264.6253-0.5909-3.51433.63014.9718.46520.12360.185-0.3189-0.1627-0.1778-0.25660.14480.36910.07820.36330.1128-0.02930.54630.03630.272257.4019231.488576.8247
274.97185.40525.87755.91696.61657.3158-0.34470.45830.112-0.72380.3882-0.7335-0.39111.2679-0.03170.40140.06290.06030.74350.13040.485369.4227242.082579.4693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 28 )A3 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 85 )A29 - 85
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 126 )A86 - 126
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 172 )A127 - 172
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 221 )A173 - 221
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 15 )B3 - 15
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 28 )B16 - 28
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 52 )B29 - 52
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 66 )B53 - 66
10X-RAY DIFFRACTION10chain 'B' and (resid 67 through 85 )B67 - 85
11X-RAY DIFFRACTION11chain 'B' and (resid 86 through 126 )B86 - 126
12X-RAY DIFFRACTION12chain 'B' and (resid 127 through 221 )B127 - 221
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 15 )C3 - 15
14X-RAY DIFFRACTION14chain 'C' and (resid 16 through 28 )C16 - 28
15X-RAY DIFFRACTION15chain 'C' and (resid 29 through 85 )C29 - 85
16X-RAY DIFFRACTION16chain 'C' and (resid 86 through 172 )C86 - 172
17X-RAY DIFFRACTION17chain 'C' and (resid 173 through 202 )C173 - 202
18X-RAY DIFFRACTION18chain 'C' and (resid 203 through 224 )C203 - 224
19X-RAY DIFFRACTION19chain 'D' and (resid 3 through 28 )D3 - 28
20X-RAY DIFFRACTION20chain 'D' and (resid 29 through 52 )D29 - 52
21X-RAY DIFFRACTION21chain 'D' and (resid 53 through 95 )D53 - 95
22X-RAY DIFFRACTION22chain 'D' and (resid 96 through 126 )D96 - 126
23X-RAY DIFFRACTION23chain 'D' and (resid 127 through 144 )D127 - 144
24X-RAY DIFFRACTION24chain 'D' and (resid 145 through 159 )D145 - 159
25X-RAY DIFFRACTION25chain 'D' and (resid 160 through 187 )D160 - 187
26X-RAY DIFFRACTION26chain 'D' and (resid 188 through 202 )D188 - 202
27X-RAY DIFFRACTION27chain 'D' and (resid 203 through 221 )D203 - 221

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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