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- PDB-8de0: TEM-1 beta-lactamase covalently bound to avibactam -

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Basic information

Entry
Database: PDB / ID: 8de0
TitleTEM-1 beta-lactamase covalently bound to avibactam
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE/INHIBITOR / Hydrolase / Beta-lactamase / TEM / avibactam / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-NXL / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsJi, Z. / Boxer, S.G. / Mathews, I.I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Protein Electric Fields Enable Faster and Longer-Lasting Covalent Inhibition of beta-Lactamases.
Authors: Ji, Z. / Kozuch, J. / Mathews, I.I. / Diercks, C.S. / Shamsudin, Y. / Schulz, M.A. / Boxer, S.G.
History
DepositionJun 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: 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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase TEM
B: Beta-lactamase TEM
C: Beta-lactamase TEM
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9458
Polymers115,8764
Non-polymers1,0694
Water19,2221067
1
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2362
Polymers28,9691
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2362
Polymers28,9691
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2362
Polymers28,9691
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2362
Polymers28,9691
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.650, 83.690, 95.570
Angle α, β, γ (deg.)90.000, 90.190, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 27 through 62 or resid 64...
21(chain B and (resid 27 through 62 or resid 64...
31(chain C and (resid 27 through 62 or resid 64...
41(chain D and (resid 27 through 62 or resid 64...

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
11PROPROPROPRO(chain A and (resid 27 through 62 or resid 64...AA27 - 623 - 38
12GLUGLULEULEU(chain A and (resid 27 through 62 or resid 64...AA64 - 8140 - 57
13ARGARGASPASP(chain A and (resid 27 through 62 or resid 64...AA83 - 21459 - 190
14VALVALGLYGLY(chain A and (resid 27 through 62 or resid 64...AA216 - 241192 - 217
15ARGARGARGARG(chain A and (resid 27 through 62 or resid 64...AA243 - 257219 - 233
16VALVALTRPTRP(chain A and (resid 27 through 62 or resid 64...AA259 - 288235 - 264
17NXLNXLNXLNXL(chain A and (resid 27 through 62 or resid 64...AE301
21PROPROPROPRO(chain B and (resid 27 through 62 or resid 64...BB27 - 623 - 38
22GLUGLULEULEU(chain B and (resid 27 through 62 or resid 64...BB64 - 8140 - 57
23ARGARGASPASP(chain B and (resid 27 through 62 or resid 64...BB83 - 21459 - 190
24VALVALGLYGLY(chain B and (resid 27 through 62 or resid 64...BB216 - 241192 - 217
25ARGARGARGARG(chain B and (resid 27 through 62 or resid 64...BB243 - 257219 - 233
26VALVALTRPTRP(chain B and (resid 27 through 62 or resid 64...BB259 - 288235 - 264
27NXLNXLNXLNXL(chain B and (resid 27 through 62 or resid 64...BF301
31PROPROPROPRO(chain C and (resid 27 through 62 or resid 64...CC27 - 623 - 38
32GLUGLULEULEU(chain C and (resid 27 through 62 or resid 64...CC64 - 8140 - 57
33ARGARGASPASP(chain C and (resid 27 through 62 or resid 64...CC83 - 21459 - 190
34VALVALGLYGLY(chain C and (resid 27 through 62 or resid 64...CC216 - 241192 - 217
35ARGARGARGARG(chain C and (resid 27 through 62 or resid 64...CC243 - 257219 - 233
36VALVALTRPTRP(chain C and (resid 27 through 62 or resid 64...CC259 - 288235 - 264
37NXLNXLNXLNXL(chain C and (resid 27 through 62 or resid 64...CG301
41PROPROPROPRO(chain D and (resid 27 through 62 or resid 64...DD27 - 623 - 38
42GLUGLULEULEU(chain D and (resid 27 through 62 or resid 64...DD64 - 8140 - 57
43ARGARGASPASP(chain D and (resid 27 through 62 or resid 64...DD83 - 21459 - 190
44VALVALGLYGLY(chain D and (resid 27 through 62 or resid 64...DD216 - 241192 - 217
45ARGARGARGARG(chain D and (resid 27 through 62 or resid 64...DD243 - 257219 - 233
46VALVALTRPTRP(chain D and (resid 27 through 62 or resid 64...DD259 - 288235 - 264
47NXLNXLNXLNXL(chain D and (resid 27 through 62 or resid 64...DH301

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Components

#1: Protein
Beta-lactamase TEM / TEM-1


Mass: 28968.955 Da / Num. of mol.: 4 / Mutation: M182T
Source method: isolated from a genetically manipulated source
Details: An extra glycine at the N-terminus / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaTEM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical
ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1067 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG3350, HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.72→38.33 Å / Num. obs: 99749 / % possible obs: 99 % / Redundancy: 13.511 % / Biso Wilson estimate: 21.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.19 / Rrim(I) all: 0.197 / Χ2: 0.83 / Net I/σ(I): 9.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.73-1.7711.2071.6471.6280924739172210.6711.72497.7
1.77-1.8213.3941.3462.2594040714570210.8011.39998.3
1.82-1.8814.0711.1792.6896106694268300.8581.22398.4
1.88-1.9313.8720.9053.4592140673566420.9080.93998.6
1.93-213.2950.7124.1686301657664910.9320.74198.7
2-2.0713.8740.5955.0486973635162690.9570.61898.7
2.07-2.1513.7760.4766.0883149610460360.9670.49498.9
2.15-2.2313.5830.3837.1279585591858590.9830.39899
2.23-2.3314.1290.3388.0679377565856180.9850.35199.3
2.33-2.4513.9550.2958.874728539453550.9890.30699.3
2.45-2.5813.1850.23910.1167585515151260.9890.24999.5
2.58-2.7413.9330.21211.5567353485648340.9930.2299.5
2.74-2.9213.6850.17613.0362487457945660.9940.18399.7
2.92-3.1614.1230.15315.3160290427742690.9950.15999.8
3.16-3.4613.7990.12217.8453956391639100.9960.12799.8
3.46-3.8712.8090.10319.9345845357935790.9970.107100
3.87-4.4713.4470.0922.7742224314031400.9980.094100
4.47-5.4714.0520.0824.8937787269026890.9980.083100
5.47-7.7412.8270.08322.926731208520840.9980.087100
7.74-38.3313.7190.05731.0115859117011560.9990.05998.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ERM

1erm


Resolution: 1.72→38.33 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 5045 5.06 %
Rwork0.1727 94704 -
obs0.1741 99749 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.75 Å2 / Biso mean: 22.4472 Å2 / Biso min: 11.91 Å2
Refinement stepCycle: final / Resolution: 1.72→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8064 0 68 1067 9199
Biso mean--21.92 32.63 -
Num. residues----1048
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4933X-RAY DIFFRACTION10.241TORSIONAL
12B4933X-RAY DIFFRACTION10.241TORSIONAL
13C4933X-RAY DIFFRACTION10.241TORSIONAL
14D4933X-RAY DIFFRACTION10.241TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.740.21411180.16042557267580
1.74-1.770.18291600.142731503310100
1.77-1.790.17631740.136932013375100
1.79-1.810.1861900.145830853275100
1.81-1.830.19211750.133831883363100
1.83-1.860.1911660.147831773343100
1.86-1.880.2011580.153831583316100
1.88-1.910.21551670.158431903357100
1.91-1.940.20731590.157331673326100
1.94-1.970.20191600.139231583318100
1.97-2.010.18711510.142232053356100
2.01-2.050.17191670.154531803347100
2.05-2.080.22141720.153931603332100
2.08-2.130.20691660.152331553321100
2.13-2.170.19491720.138232023374100
2.17-2.220.18761920.142831403332100
2.22-2.280.18511650.153731533318100
2.28-2.340.20351620.16332113373100
2.34-2.410.16961570.161931863343100
2.41-2.490.20741850.165231073292100
2.49-2.580.22041560.158732273383100
2.58-2.680.18361740.165931663340100
2.68-2.80.24281630.182331713334100
2.8-2.950.21681860.195831803366100
2.95-3.130.24111740.198731943368100
3.13-3.380.21941710.178431863357100
3.38-3.720.16611620.173932053367100
3.72-4.250.17191830.166431883371100
4.25-5.360.16971900.182532123402100
5.36-38.330.24461700.24673245341599

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