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- PDB-9d7d: OXA-58-NA-1-157 20 min complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9d7d
TitleOXA-58-NA-1-157 20 min complex
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / beta-lactamase / carbapenemase / antibiotic resistance / inhibitor / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
ACETATE ION / CARBON DIOXIDE / Chem-Y33 / Beta-lactamase OXA-58
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsSmith, C.A. / Maggiolo, A.O. / Toth, M. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI155723 United States
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Decarboxylation of the Catalytic Lysine Residue by the C5 alpha-Methyl-Substituted Carbapenem NA-1-157 Leads to Potent Inhibition of the OXA-58 Carbapenemase.
Authors: Toth, M. / Stewart, N.K. / Maggiolo, A.O. / Quan, P. / Khan, M.M.K. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B.
History
DepositionAug 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)127,57411
Polymers125,8214
Non-polymers1,7537
Water3,225179
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9013
Polymers31,4551
Non-polymers4452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9163
Polymers31,4551
Non-polymers4612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9013
Polymers31,4551
Non-polymers4452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8572
Polymers31,4551
Non-polymers4011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.930, 66.584, 193.460
Angle α, β, γ (deg.)90.00, 91.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase


Mass: 31455.205 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-58, bla-oxa-58, bla-oxa58, GSE42_20550, P9867_20895
Production host: Escherichia coli (E. coli) / References: UniProt: Q2TR58, beta-lactamase
#2: Chemical
ChemComp-Y33 / (5R)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid


Mass: 401.478 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 0.1 M Tris-HCl pH 8.5, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→39.12 Å / Num. obs: 56857 / % possible obs: 96.4 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rpim(I) all: 0.058 / Rrim(I) all: 0.156 / Net I/σ(I): 8.8
Reflection shellResolution: 2.05→2.11 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4358 / CC1/2: 0.585 / Rpim(I) all: 0.594

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→39.12 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 2758 4.86 %
Rwork0.1838 --
obs0.1862 56782 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7874 0 4 179 8057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078055
X-RAY DIFFRACTIONf_angle_d1.01310907
X-RAY DIFFRACTIONf_dihedral_angle_d18.622990
X-RAY DIFFRACTIONf_chiral_restr0.0551178
X-RAY DIFFRACTIONf_plane_restr0.0071409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.3191450.28312599X-RAY DIFFRACTION95
2.09-2.120.3391350.26472690X-RAY DIFFRACTION97
2.12-2.160.29281600.2412742X-RAY DIFFRACTION97
2.16-2.210.28571320.23882674X-RAY DIFFRACTION97
2.21-2.260.29361290.23072685X-RAY DIFFRACTION96
2.26-2.310.24671430.22672660X-RAY DIFFRACTION92
2.31-2.370.26181160.22192455X-RAY DIFFRACTION90
2.37-2.430.29571210.22152735X-RAY DIFFRACTION98
2.43-2.50.27131410.21732735X-RAY DIFFRACTION98
2.5-2.580.28961240.22012763X-RAY DIFFRACTION98
2.58-2.670.29761480.21552750X-RAY DIFFRACTION98
2.68-2.780.26271350.20352761X-RAY DIFFRACTION98
2.78-2.910.26691300.20112748X-RAY DIFFRACTION98
2.91-3.060.23471460.2092762X-RAY DIFFRACTION97
3.06-3.250.27451300.20642642X-RAY DIFFRACTION95
3.25-3.50.22051450.17572556X-RAY DIFFRACTION90
3.51-3.860.20671560.16332774X-RAY DIFFRACTION99
3.86-4.410.17191320.13782800X-RAY DIFFRACTION99
4.42-5.560.17451530.13592767X-RAY DIFFRACTION97
5.56-39.120.21221370.15062726X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.26430.1253-0.07490.1434-0.15560.19020.1617-0.72180.07950.6520.1813-0.4320.05630.50830.00160.5643-0.0880.00430.82440.12270.5343-14.5748-6.243886.5032
21.42290.51610.33410.67060.51011.4030.0567-0.25210.09650.0116-0.0529-0.2077-0.11220.31110.00010.3082-0.03140.00860.39410.01550.2905-18.62361.345569.6288
32.71970.08220.49860.97010.78671.90010.07210.2893-0.35760.1412-0.015-0.0775-0.0244-0.0731-0.00010.32820.0259-0.01660.4009-0.080.3148-30.4152-5.144251.8094
42.4073-0.36641.2011.236-0.63873.19940.0968-0.0875-0.2381-0.054-0.05350.0452-0.18220.01420.00010.3282-0.00720.00440.3065-0.02190.2791-25.60740.50364.461
50.73220.74330.6211.5975-0.12361.1684-0.2445-0.7274-0.49280.43240.0970.12680.24650.1875-0.00040.3530.00280.03770.55770.04180.3073-23.7795-1.278174.8992
60.4557-0.02160.17180.4928-0.49550.53370.0771-0.5282-0.78630.1809-0.09280.06160.5450.0924-0.00090.4156-0.0204-0.03130.53170.10630.472-22.3801-10.704977.5319
71.7080.31580.20251.27670.2521.34780.06530.1180.21-0.1023-0.08120.2727-0.0501-0.27390.00020.27210.02610.03390.2080.00050.306-19.3405-28.955119.894
81.8361-0.13130.62691.7273-0.69822.20410.0657-0.3496-0.10460.0271-0.0296-0.1580.09780.1317-0.00010.2977-0.03170.03830.2916-0.01970.3076-6.4267-31.845141.9871
91.77150.3536-0.06561.03330.72552.640.020.0169-0.0314-0.00180.0142-0.0115-0.10620.00660.00010.2740.01110.00770.18020.00370.2943-11.3949-27.352928.8208
101.5082-0.77740.39631.27030.45681.97370.05440.1854-0.1709-0.1353-0.05520.00930.15820.1952-0.00020.2536-0.0198-0.0060.2587-0.01560.3404-14.0986-36.241117.2937
110.08940.0647-0.0040.1384-0.05620.309-0.048-0.8294-0.1017-0.16770.33380.87980.4151-1.2345-0.00170.44260.0221-0.04540.6019-0.02990.3875-6.56235.382940.1431
120.86910.5938-0.19460.5054-0.5251.3848-0.0377-0.003-0.1088-0.0237-0.00510.08360.0217-0.11560.00020.26720.0009-0.02250.1931-0.0030.2719-2.3143-0.705822.5399
132.5527-0.42710.29011.2851-0.39610.6564-0.20090.3120.3125-0.20750.1105-0.0294-0.10530.1288-0.00020.3665-0.0231-0.02820.32930.03370.26239.36717.11365.2085
141.8017-0.5025-0.63060.67880.41451.396-0.00340.02640.0943-0.058-0.01610.07560.0705-0.0016-0.00010.2927-0.0106-0.01830.1740.02010.26394.63280.573217.5098
150.9651.0148-0.93291.3189-0.74441.0945-0.2411-0.46840.22530.34890.1388-0.2036-0.0471-0.0788-0.00010.253-0.0122-0.0590.2471-0.06710.27272.86681.612727.971
160.80530.7643-0.18370.89850.13760.5784-0.1626-0.30630.41410.23090.04980.1749-0.2698-0.1854-0.00040.31080.03-0.01040.2463-0.06150.32451.326110.623131.5697
171.2814-1.4594-0.96871.73431.18290.83420.51010.55940.6418-0.76060.0104-0.5511-0.05450.45360.14070.5990.16170.07150.64080.1830.45241.390626.401958.3952
181.1587-0.03790.18121.02230.77541.5971-0.0680.04270.09670.1524-0.0183-0.24080.3710.3045-0.00010.32930.010.02130.4935-0.01360.3317-2.025924.822477.2656
191.2063-0.04340.40550.22090.11870.6878-0.1931-0.33510.9586-0.0325-0.2477-0.1664-0.4051-0.3963-0.03030.54270.0188-0.01780.7512-0.18760.6752-16.023840.233693.8257
201.07450.65020.30310.87310.87731.1473-0.2851-0.44580.12350.10880.11250.00560.1537-0.33850.00010.45520.03450.04960.4948-0.10530.3498-12.430731.761292.9531
210.27260.0351-0.27060.2296-0.17960.3489-0.1605-0.34960.18120.25310.0388-0.06160.31820.7225-0.00010.44560.05640.00120.5483-0.06930.3651-0.78127.075992.5834
221.514-0.04430.24591.2282-0.26591.71320.05910.29010.3420.1278-0.1160.25220.1198-0.44440.00030.3575-0.05810.01960.4956-0.05130.4178-14.887825.230678.0776
230.4907-0.2594-0.35780.4684-0.24470.8297-0.0723-0.09860.6417-0.206-0.1007-0.3054-0.2351-0.0601-0.00080.31570.02160.02790.5055-0.07730.4758-2.417731.835378.8613
240.7182-0.5828-0.52181.0152-0.31521.3643-0.09260.40550.3239-0.54260.12750.1399-0.17340.0981-0.00040.4262-0.0376-0.01160.47650.03650.5058-4.399431.400372.5122
250.2265-0.0565-0.1880.11010.2340.49290.27170.61880.5714-0.7323-0.10930.0212-0.6518-1.37220.00510.39550.03590.01830.7010.13840.4601-8.115132.338264.222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 154 )
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 239 )
5X-RAY DIFFRACTION5chain 'A' and (resid 240 through 254 )
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 280 )
7X-RAY DIFFRACTION7chain 'B' and (resid 38 through 95 )
8X-RAY DIFFRACTION8chain 'B' and (resid 96 through 154 )
9X-RAY DIFFRACTION9chain 'B' and (resid 155 through 239 )
10X-RAY DIFFRACTION10chain 'B' and (resid 240 through 280 )
11X-RAY DIFFRACTION11chain 'C' and (resid 38 through 50 )
12X-RAY DIFFRACTION12chain 'C' and (resid 51 through 95 )
13X-RAY DIFFRACTION13chain 'C' and (resid 96 through 154 )
14X-RAY DIFFRACTION14chain 'C' and (resid 155 through 239 )
15X-RAY DIFFRACTION15chain 'C' and (resid 240 through 254 )
16X-RAY DIFFRACTION16chain 'C' and (resid 255 through 280 )
17X-RAY DIFFRACTION17chain 'D' and (resid 36 through 50 )
18X-RAY DIFFRACTION18chain 'D' and (resid 51 through 95 )
19X-RAY DIFFRACTION19chain 'D' and (resid 96 through 117 )
20X-RAY DIFFRACTION20chain 'D' and (resid 118 through 154 )
21X-RAY DIFFRACTION21chain 'D' and (resid 155 through 177 )
22X-RAY DIFFRACTION22chain 'D' and (resid 178 through 224 )
23X-RAY DIFFRACTION23chain 'D' and (resid 225 through 239 )
24X-RAY DIFFRACTION24chain 'D' and (resid 240 through 261 )
25X-RAY DIFFRACTION25chain 'D' and (resid 262 through 280 )

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