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- PDB-7jqy: Crystal structure of Cfl1-D123S from Burkholderia cenocepacia -

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Basic information

Entry
Database: PDB / ID: 7jqy
TitleCrystal structure of Cfl1-D123S from Burkholderia cenocepacia
ComponentsCif-like 1
KeywordsHYDROLASE / Octamer / alpha/beta hydrolase fold
Function / homologyEpoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Hydrolase
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsTaher, N.M. / Madden, D.R.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI091699 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM113240 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37-AI83256-06 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20-GM113132 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30-DK117469 United States
Cystic Fibrosis FoundationSTANTO19R0 United States
CitationJournal: Curr Res Struct Biol / Year: 2021
Title: Biochemical and structural characterization of two cif-like epoxide hydrolases from Burkholderia cenocepacia .
Authors: Taher, N.M. / Hvorecny, K.L. / Burke, C.M. / Gilman, M.S.A. / Heussler, G.E. / Adolf-Bryfogle, J. / Bahl, C.D. / O'Toole, G.A. / Madden, D.R.
History
DepositionAug 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 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: Cif-like 1
B: Cif-like 1
C: Cif-like 1
D: Cif-like 1
E: Cif-like 1
F: Cif-like 1
G: Cif-like 1
H: Cif-like 1


Theoretical massNumber of molelcules
Total (without water)276,0918
Polymers276,0918
Non-polymers00
Water14,178787
1
A: Cif-like 1
B: Cif-like 1

A: Cif-like 1
B: Cif-like 1

G: Cif-like 1

G: Cif-like 1

E: Cif-like 1

E: Cif-like 1


Theoretical massNumber of molelcules
Total (without water)276,0918
Polymers276,0918
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_566-x,y+1,-z+11
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area18080 Å2
ΔGint-103 kcal/mol
Surface area79670 Å2
MethodPISA
2
C: Cif-like 1
D: Cif-like 1
F: Cif-like 1
H: Cif-like 1

C: Cif-like 1
D: Cif-like 1
F: Cif-like 1
H: Cif-like 1


Theoretical massNumber of molelcules
Total (without water)276,0918
Polymers276,0918
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18110 Å2
ΔGint-106 kcal/mol
Surface area79450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.000, 98.400, 170.000
Angle α, β, γ (deg.)90.000, 118.600, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-426-

HOH

21D-445-

HOH

31H-429-

HOH

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Components

#1: Protein
Cif-like 1


Mass: 34511.316 Da / Num. of mol.: 8 / Mutation: D123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAM1529 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EJL9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 6% ethylene glycol, 8% PEG 8000, 100 mM HEPES pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.15→49.367 Å / Num. obs: 152155 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 10.96
Reflection shellResolution: 2.15→2.28 Å / Num. unique obs: 23995 / CC1/2: 0.781

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2

3kd2


Resolution: 2.15→44.71 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 7615 5.01 %
Rwork0.2089 144390 -
obs0.2104 152005 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.71 Å2 / Biso mean: 57.0318 Å2 / Biso min: 23.78 Å2
Refinement stepCycle: final / Resolution: 2.15→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18502 0 0 787 19289
Biso mean---45.61 -
Num. residues----2348
LS refinement shellResolution: 2.15→2.18 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4105 379 -
Rwork0.3516 4177 -
obs--90 %
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)
10.0256-0.0007-0.0255-0.00180.00790.00710.036-0.0077-0.13490.1216-0.0195-0.00960.0692-0.031-00.4480.0208-0.05330.33570.01760.3222-22.79338.486572.596
20.0287-0.0002-0.01860.0024-0.02790.01520.0183-0.02480.02690.014-0.0224-0.1328-0.01860.116200.29640.044-0.04620.28980.00530.3155-11.475316.015773.9595
30.10360.0586-0.00970.1180.08390.14730.00170.05930.08480.00310.007-0.04880.03740.0075-00.3115-0.0001-0.00370.26610.00940.3037-13.359124.552365.2504
40.0136-0.0145-0.00440.02620.0230.0289-0.01010.07410.0689-0.10590.0238-0.07280.06580.0623-00.32130.01820.00120.32790.00670.2803-8.804314.448354.0608
50.01490.01350.02430.0090.01520.01640.0053-0.0933-0.0338-0.0578-0.05360.0020.1583-0.0131-00.438-0.0202-0.04070.35710.00960.3052-39.08058.479291.9389
60.02820.02870.02520.0103-0.01960.03960.0788-0.1987-0.0460.0627-0.0586-0.0393-0.0105-0.0636-00.3395-0.0297-0.02820.33020.01820.1708-37.82912.0375101.5094
70.11530.06860.04210.0805-0.07010.07870.0387-0.28130.2473-0.0186-0.0117-0.01590.0276-0.014800.2410.0222-0.03610.3597-0.07750.1964-30.844325.9548101.982
80.0233-0.00980.0053-0.00090.01120.01110.0508-0.2624-0.038-0.005-0.0564-0.23580.10320.1551-00.37850.0127-0.07610.47490.0170.2974-20.090813.0608105.4027
90.0090.0102-0.01970.00120.00630.0007-0.0181-0.0626-0.01850.0454-0.0574-0.10660.00280.171900.42380.0256-0.02690.5882-0.06650.38338.2671-2.111132.4628
100.0099-0.0035-0.0090.005-0.02320.0048-0.0208-0.0369-0.11550.02740.0614-0.02620.12280.040100.39330.0348-0.00690.32780.02570.2818-2.26-9.788732.0732
110.0468-0.0224-0.11130.08660.07980.15580.03350.0565-0.03870.0530.03040.06190.0442-0.038800.39430.01290.03090.3516-0.00960.3178-11.3348-4.417430.3394
120.0217-0.0955-0.01550.040.03190.0830.0070.04670.02360.00930.02680.01310.0236-0.111700.3691-0.02540.01560.3835-0.01550.3297-12.09962.196527.5282
130.0097-0.0096-0.01480.01880.01750.0149-0.0459-0.0644-0.0210.1910.06770.02460.05530.009200.39280.00880.01880.3563-0.00610.2901-11.43253.88943.4623
140.01550.00410.01880.00450.00970.0130.0035-0.06090.03340.0960.1015-0.0787-0.02740.03700.36810.0728-0.060.9113-0.02660.379227.22-4.915217.4798
150.00870.00150.00210.0315-0.002-0.00530.02270.03490.0016-0.02020.0763-0.14010.10310.243900.36980.2008-0.01560.8019-0.02330.308929.1184-12.93710.8021
160.0476-0.0219-0.05540.026-0.03180.1622-0.1374-0.08630.1693-0.01340.08030.10320.19340.4103-00.41280.1270.05940.48600.23916.4265-16.67323.8118
170.02420.01040.00330.0072-0.0190.0193-0.0735-0.2336-0.16520.0337-0.0044-0.04280.3230.2431-00.63350.2720.04010.57010.0780.369519.8253-28.198112.3701
180.0093-0.0194-0.00320.00810.00790.02330.0386-0.03290.13710.1141-0.1205-0.12630.0696-0.142900.45830.0688-0.12660.27710.01441.241636.876917.652872.054
190.00470.00360.0219-0.0022-0.01210.0355-0.1858-0.05280.49260.0661-0.1147-0.13610.4914-0.44-0-0.18960.5384-0.1867-0.40840.15250.992627.05912.084267.8907
200.0385-0.0666-0.02950.07060.007-0.02040.04760.19170.34650.0252-0.0963-0.06520.0718-0.047800.30030.011-0.01310.2650.13290.647733.85290.257759.348
210.01340.00450.01580.0287-0.01040.0284-0.03320.11360.1365-0.1028-0.0397-0.1912-0.023-0.1482-00.3180.1641-0.11070.26480.46221.15927.636515.213551.1471
220.00330.00190.00050.0032-0.00690.00010.10340.0474-0.0596-0.02050.04790.0624-0.1587-0.1413-00.55010.19410.02180.85980.22760.4775-30.305519.3184-14.9088
230.0214-0.0114-0.02050.0117-0.00970.01650.17120.05810.06760.0290.1353-0.0374-0.3079-0.1703-00.47870.6459-0.02850.91320.42080.1574-34.084924.8967-6.8397
240.03220.0289-0.05170.0444-0.00030.09550.25320.1957-0.18050.04550.0858-0.1021-0.2701-0.5361-00.430.2120.15340.65390.12130.2309-29.035620.00987.0935
250.02320.0029-0.01070.0124-0.01210.01170.09630.09040.0152-0.02190.13580.0420.0122-0.1741-00.22310.3120.07751.36080.18450.4588-44.56714.26283.4335
260.0008-0.0150.00260.0172-0.02020.0019-0.04950.09910.2468-0.048-0.0867-0.1257-0.0332-0.1053-0-0.1530.772-0.503-1.111.37821.2779-35.713-31.291950.8253
27-0.0245-0.01060.05840.0749-0.02510.0005-0.23980.46180.83570.1227-0.0265-0.20710.1801-0.080500.1847-0.1880.0603-1.29951.71750.211-28.1906-46.403248.3554
280.0040.0205-0.02820.0137-0.01410.0027-0.10490.06260.2456-0.0460.0838-0.0813-0.00460.1485-0-0.0189-0.58240.233-0.06141.19761.3777-17.213-33.678146.1005
29-0.0039-0.00220.01470.06010.00320.03570.1434-0.1838-0.1860.06070.13490.0129-0.23780.2149-00.8034-0.25310.18970.5123-0.22170.25976.61528.863230.6691
300.0394-0.01070.02150.0262-0.00950.04930.57640.1095-0.1687-0.02420.33190.1884-0.61020.265800.9448-0.13710.50740.2233-0.00020.1933-0.357636.083216.8436
31-0.00590.0082-0.00240.019-0.0018-0.0020.08810.01070.05620.0010.1076-0.0174-0.11360.0764-01.3923-0.84480.3896-0.1012-0.61380.30212.05246.00923.2627
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 32 )A11 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 60 )A33 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 243 )A61 - 243
4X-RAY DIFFRACTION4chain 'A' and (resid 244 through 303 )A244 - 303
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 32 )B11 - 32
6X-RAY DIFFRACTION6chain 'B' and (resid 33 through 82 )B33 - 82
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 243 )B83 - 243
8X-RAY DIFFRACTION8chain 'B' and (resid 244 through 304 )B244 - 304
9X-RAY DIFFRACTION9chain 'C' and (resid 12 through 32 )C12 - 32
10X-RAY DIFFRACTION10chain 'C' and (resid 33 through 60 )C33 - 60
11X-RAY DIFFRACTION11chain 'C' and (resid 61 through 186 )C61 - 186
12X-RAY DIFFRACTION12chain 'C' and (resid 187 through 259 )C187 - 259
13X-RAY DIFFRACTION13chain 'C' and (resid 260 through 304 )C260 - 304
14X-RAY DIFFRACTION14chain 'D' and (resid 11 through 32 )D11 - 32
15X-RAY DIFFRACTION15chain 'D' and (resid 33 through 82 )D33 - 82
16X-RAY DIFFRACTION16chain 'D' and (resid 83 through 230 )D83 - 230
17X-RAY DIFFRACTION17chain 'D' and (resid 231 through 304 )D231 - 304
18X-RAY DIFFRACTION18chain 'E' and (resid 11 through 36 )E11 - 36
19X-RAY DIFFRACTION19chain 'E' and (resid 37 through 135 )E37 - 135
20X-RAY DIFFRACTION20chain 'E' and (resid 136 through 243 )E136 - 243
21X-RAY DIFFRACTION21chain 'E' and (resid 244 through 304 )E244 - 304
22X-RAY DIFFRACTION22chain 'F' and (resid 11 through 32 )F11 - 32
23X-RAY DIFFRACTION23chain 'F' and (resid 33 through 82 )F33 - 82
24X-RAY DIFFRACTION24chain 'F' and (resid 83 through 243 )F83 - 243
25X-RAY DIFFRACTION25chain 'F' and (resid 244 through 303 )F244 - 303
26X-RAY DIFFRACTION26chain 'G' and (resid 11 through 81 )G11 - 81
27X-RAY DIFFRACTION27chain 'G' and (resid 82 through 243 )G82 - 243
28X-RAY DIFFRACTION28chain 'G' and (resid 244 through 303 )G244 - 303
29X-RAY DIFFRACTION29chain 'H' and (resid 11 through 82 )H11 - 82
30X-RAY DIFFRACTION30chain 'H' and (resid 83 through 243 )H83 - 243
31X-RAY DIFFRACTION31chain 'H' and (resid 244 through 304 )H244 - 304

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