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- PDB-6wif: Class C beta-lactamase from Acinetobacter baumannii in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6wif
TitleClass C beta-lactamase from Acinetobacter baumannii in complex with 4-(Ethyl(methyl)carbamoyl)phenyl boronic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / class C beta-lactamase / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / HYDROLASE / HYDROLASE-INHIBITOR complex / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
{4-[ethyl(methyl)carbamoyl]phenyl}boronic acid / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChang, C. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: class C beta-lactamase from Acinetobacter baumannii in complex with 4-(Ethyl(methyl)carbamoyl)phenyl boronic acid
Authors: Chang, C. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)164,65526
Polymers162,0854
Non-polymers2,57022
Water11,998666
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7643
Polymers40,5211
Non-polymers2422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1536
Polymers40,5211
Non-polymers6325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4629
Polymers40,5211
Non-polymers9418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2778
Polymers40,5211
Non-polymers7567
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.244, 80.925, 104.377
Angle α, β, γ (deg.)90.000, 113.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase /


Mass: 40521.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ampC, A7M79_07980, A7M90_05015, BGC29_02775, E5294_06010, FJU36_01670, LV38_01949
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D6NSN2, beta-lactamase

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Non-polymers , 5 types, 688 molecules

#2: Chemical
ChemComp-U2Y / {4-[ethyl(methyl)carbamoyl]phenyl}boronic acid


Mass: 207.034 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14BNO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M Sodium Chloride, 0.1M HEPES, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 76937 / % possible obs: 99.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.028 / Rrim(I) all: 0.062 / Χ2: 0.937 / Net I/σ(I): 10.5 / Num. measured all: 363992
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.193.20.57934560.7330.3580.6870.91389
2.19-2.233.40.54536650.7830.3280.6420.92595.5
2.23-2.273.80.48238570.8410.2760.5580.999.8
2.27-2.324.10.45838580.8690.2510.5240.933100
2.32-2.374.40.40338740.9130.2140.4580.939100
2.37-2.424.80.3538520.9320.1760.3930.929100
2.42-2.4850.30138440.9540.1490.3360.942100
2.48-2.5550.25538460.9670.1260.2850.961100
2.55-2.6250.21138730.9760.1040.2350.955100
2.62-2.715.10.19138630.9780.0940.2140.957100
2.71-2.815.10.14838800.9880.0720.1650.996100
2.81-2.925.10.12138500.9910.0590.1340.994100
2.92-3.055.10.09638790.9930.0470.1071.017100
3.05-3.215.10.07238940.9960.0350.0811.02100
3.21-3.415.10.05238520.9970.0250.0581.004100
3.41-3.685.10.04138970.9980.0190.0450.988100
3.68-4.055.10.03239010.9980.0160.0360.914100
4.05-4.635.10.02738730.9990.0130.030.788100
4.63-5.8350.02539450.9990.0120.0280.691100
5.83-504.80.0339780.9980.0150.0340.93899.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SBC-Collectdata collection
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QD4
Resolution: 2.15→43.38 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.41
RfactorNum. reflection% reflection
Rfree0.2396 3532 4.88 %
Rwork0.1927 --
obs0.1949 72421 93.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.92 Å2 / Biso mean: 35.1827 Å2 / Biso min: 5.54 Å2
Refinement stepCycle: final / Resolution: 2.15→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11320 0 167 666 12153
Biso mean--50.14 35.14 -
Num. residues----1428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.180.2519850.23711400148548
2.18-2.210.2963810.25171701178258
2.21-2.240.28171150.24392107222272
2.24-2.280.30661220.23672347246980
2.28-2.320.29011430.24932531267487
2.32-2.360.25761380.24252700283892
2.36-2.40.31361350.24782889302498
2.4-2.450.28871410.2422950309199
2.45-2.50.29651500.237428833033100
2.5-2.550.2841620.239929613123100
2.55-2.610.31531460.225829503096100
2.61-2.670.27991450.229229603105100
2.67-2.750.25931460.228229563102100
2.75-2.830.27031870.217629093096100
2.83-2.920.2471710.227528953066100
2.92-3.020.27331500.219429573107100
3.02-3.140.25891550.222129363091100
3.14-3.290.25421630.199329473110100
3.29-3.460.24281470.197229543101100
3.46-3.680.22351350.176929933128100
3.68-3.960.23551390.161529513090100
3.96-4.360.17041430.149229953138100
4.36-4.990.16971300.139829943124100
4.99-6.280.20031540.154929943148100
6.28-43.380.18511490.14823029317899
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)
10.4127-0.21620.03460.7365-0.27630.26880.1290.11030.2235-0.1542-0.1208-0.23990.01090.10210.01670.65740.12970.30170.1790.1290.410318.66316.0293-5.2557
20.56030.3974-0.09870.7833-0.17320.31340.116-0.03240.07140.0367-0.0735-0.1292-0.00460.03990.30710.3663-0.00690.24770.1130.05830.438225.63713.2272.922
30.8644-0.30560.04641.333-0.13280.19760.2375-0.2870.21250.1059-0.1145-0.15140.08410.0511-0.03270.4446-0.08810.10580.1762-0.03740.221515.7833-0.510613.9301
41.7528-0.00290.55070.53460.41340.49490.2098-0.4573-0.12210.2092-0.02150.11280.0215-0.0122-0.11940.7098-0.13690.01820.48540.23170.36999.9942-26.658825.6041
51.1962-0.2889-0.06190.96520.26620.54350.1141-0.451-0.25840.399-0.02810.33390.0726-0.1396-0.1020.4409-0.1410.06710.30230.06760.29255.0452-18.339519.5091
60.8133-0.5056-0.2120.6378-0.06380.20390.2142-0.34280.26730.1546-0.0897-0.01230.02350.1093-0.09060.4397-0.12720.13430.2524-0.0880.240514.30520.362116.0442
71.53710.52750.20860.8620.51741.01690.2491-0.2352-0.11030.0315-0.0525-0.14360.00920.1967-0.17430.41760.00080.00180.20820.02580.199422.6057-18.50458.9736
80.6231-0.06320.13951.08430.01020.31760.284-0.0469-0.1054-0.1219-0.2150.194-0.04220.0388-0.11360.43250.01110.04120.1097-0.00010.188813.7445-15.20060.4918
90.8511-0.61280.20371.6734-0.37250.7650.18020.08940.0506-0.226-0.1578-0.13070.20260.1122-0.0030.5350.05110.16410.1090.02940.213218.3702-4.285-1.8587
100.9998-0.180.06861.37490.29040.94050.104-0.07190.2436-0.21080.0423-0.3274-0.15350.1063-0.06420.158-0.0158-0.01110.1446-0.12790.245967.68925.40140.577
110.83180.4276-0.451.0109-0.07330.638-0.0763-0.4446-0.33480.4565-0.076-0.11740.34380.1113-0.08350.36120.0182-0.04820.32220.07980.238258.7574-23.292921.3489
121.03740.0148-0.18581.0529-0.07140.825-0.0036-0.3561-0.19110.41850.06410.19110.2365-0.0994-0.00910.2418-0.0239-0.00630.30550.03690.225751.1793-18.421418.9924
130.1305-0.0090.00240.3755-0.22980.14450.0466-0.27170.0460.286-0.0475-0.1071-0.04340.01020.08790.1602-0.0135-0.10220.3317-0.16930.243262.1391-0.880115.3023
141.52790.29290.37990.3783-0.07151.12790.0256-0.1522-0.34450.0237-0.0864-0.43070.21940.1155-0.23860.15280.054-0.11060.2054-0.00710.364367.7649-20.13957.0705
150.80690.60820.13590.46610.11340.7877-0.05640.017-0.1891-0.1116-0.00290.04960.128-0.0266-0.46750.0379-0.043-0.10190.2052-0.13370.202258.7228-15.7666-0.5783
160.80560.59330.20570.95580.0090.619-0.09280.0621-0.1287-0.0345-0.0243-0.0947-0.0129-0.0122-0.35190.0816-0.0117-0.02210.2001-0.11250.192164.7688-4.31710.8666
171.10860.59960.47951.02390.53850.8665-0.07030.1517-0.1031-0.11610.0797-0.1095-0.020.0611-0.16310.1813-0.0894-0.02040.1818-0.1570.137363.9316-5.7157-7.0627
181.16950.0025-0.08820.85550.040.8660.1746-0.3767-0.15520.19170.0723-0.16940.3960.0688-0.01110.17560.0368-0.08890.18370.03050.17446.641914.693528.4904
191.44640.3405-0.65120.523-0.08940.62040.1615-0.25870.41150.06180.09620.0748-0.3074-0.3174-0.07880.68620.18270.18790.8825-0.31880.73932.391145.394444.0289
200.4422-0.03770.08760.196-0.27770.40070.1138-0.18870.4425-0.0026-0.04040.1052-0.2256-0.1964-0.13220.39570.25570.04770.6836-0.1210.586126.333437.938933.7723
211.5019-0.4433-0.06591.2210.15820.73030.0506-0.41810.34850.1910.00820.1686-0.2078-0.3399-0.14960.29990.16960.05390.7064-0.22530.504828.15936.295839.8921
221.44470.35590.54710.61430.68821.83810.0069-0.15390.4165-0.1790.05170.0761-0.447-0.03450.04610.15550.0029-0.01580.14330.04510.258543.762430.536725.025
231.08690.14970.51061.28260.00471.94060.1275-0.65740.10780.4425-0.1898-0.1714-0.05680.0027-0.13110.1792-0.0321-0.06450.4096-0.04320.180850.61825.049841.4085
240.36510.338-0.38850.3098-0.35390.40070.2386-0.81550.00630.3505-0.10830.25570.0947-0.5635-0.00640.2232-0.21090.06970.8210.05850.175533.107918.673343.5443
250.48140.4602-0.49970.8710.17991.53420.186-0.4793-0.30930.3151-0.025-0.06460.316-0.3266-0.19310.3313-0.126-0.10650.30940.16210.227440.543510.618734.9275
261.03480.1541-0.15082.0634-0.20391.77-0.11210.3447-0.3568-0.09390.14670.25350.44-0.3458-0.17970.2685-0.0387-0.02780.2773-0.06080.280855.376-34.015667.7427
270.78680.1456-0.31511.1112-0.47490.98970.04890.32850.13770.09960.14990.1378-0.3385-0.1136-0.13170.22440.020.03290.26110.05150.153964.0137-5.784462.5508
280.74970.3296-0.25980.929-0.27081.0202-0.0290.421-0.0049-0.01620.18860.1964-0.2318-0.1717-0.09750.22330.019-0.00660.29250.01940.129759.2819-14.764662.4278
290.53080.0978-0.46970.7083-0.18830.5786-0.20390.4178-0.1551-0.30.1857-0.18080.1263-0.0426-0.10160.2593-0.0420.0390.3612-0.08970.194768.6927-21.775754.8884
301.0596-0.6613-0.06081.583-0.56492.1478-0.12490.4456-0.242-0.32320.16920.10060.25260.0297-0.18190.2049-0.0624-0.00510.2731-0.09660.185460.7931-28.989961.2047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 50 )A28 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 68 )A51 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 103 )A69 - 103
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 129 )A104 - 129
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 200 )A130 - 200
6X-RAY DIFFRACTION6chain 'A' and (resid 201 through 263 )A201 - 263
7X-RAY DIFFRACTION7chain 'A' and (resid 264 through 299 )A264 - 299
8X-RAY DIFFRACTION8chain 'A' and (resid 300 through 350 )A300 - 350
9X-RAY DIFFRACTION9chain 'A' and (resid 351 through 382 )A351 - 382
10X-RAY DIFFRACTION10chain 'B' and (resid 24 through 86 )B24 - 86
11X-RAY DIFFRACTION11chain 'B' and (resid 87 through 129 )B87 - 129
12X-RAY DIFFRACTION12chain 'B' and (resid 130 through 200 )B130 - 200
13X-RAY DIFFRACTION13chain 'B' and (resid 201 through 263 )B201 - 263
14X-RAY DIFFRACTION14chain 'B' and (resid 264 through 299 )B264 - 299
15X-RAY DIFFRACTION15chain 'B' and (resid 300 through 350 )B300 - 350
16X-RAY DIFFRACTION16chain 'B' and (resid 351 through 366 )B351 - 366
17X-RAY DIFFRACTION17chain 'B' and (resid 367 through 382 )B367 - 382
18X-RAY DIFFRACTION18chain 'C' and (resid 26 through 103 )C26 - 103
19X-RAY DIFFRACTION19chain 'C' and (resid 104 through 129 )C104 - 129
20X-RAY DIFFRACTION20chain 'C' and (resid 130 through 160 )C130 - 160
21X-RAY DIFFRACTION21chain 'C' and (resid 161 through 190 )C161 - 190
22X-RAY DIFFRACTION22chain 'C' and (resid 191 through 248 )C191 - 248
23X-RAY DIFFRACTION23chain 'C' and (resid 249 through 279 )C249 - 279
24X-RAY DIFFRACTION24chain 'C' and (resid 280 through 350 )C280 - 350
25X-RAY DIFFRACTION25chain 'C' and (resid 351 through 382 )C351 - 382
26X-RAY DIFFRACTION26chain 'D' and (resid 26 through 58 )D26 - 58
27X-RAY DIFFRACTION27chain 'D' and (resid 59 through 216 )D59 - 216
28X-RAY DIFFRACTION28chain 'D' and (resid 217 through 299 )D217 - 299
29X-RAY DIFFRACTION29chain 'D' and (resid 300 through 350 )D300 - 350
30X-RAY DIFFRACTION30chain 'D' and (resid 351 through 382 )D351 - 382

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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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