[English] 日本語
Yorodumi
- PDB-7jqy: Crystal structure of Cfl1-D123S from Burkholderia cenocepacia -

+
Open data


ID or keywords:

Loading...

-
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 / Putative 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more