[English] 日本語
Yorodumi
- PDB-5tnq: Crystal structure of the E153Q mutant of the CFTR inhibitory fact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tnq
TitleCrystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted (R)-Styrene oxide hydrolysis intermediate
ComponentsCFTR inhibitory factor
KeywordsHYDROLASE / epoxide hydrolase / hydroxyalkyl-enzyme intermediate
Function / homology
Function and homology information


Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(1R)-1-phenylethane-1,2-diol / Putative hydrolase / CFTR inhibitory factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHvorecny, K.L. / Madden, D.R.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI091699 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM106394 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)U24DK097154 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008704 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01ES002710 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)P42ES004699 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)K99ES024806 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R00ES024806 United States
CitationJournal: Structure / Year: 2017
Title: Active-Site Flexibility and Substrate Specificity in a Bacterial Virulence Factor: Crystallographic Snapshots of an Epoxide Hydrolase.
Authors: Hvorecny, K.L. / Bahl, C.D. / Kitamura, S. / Lee, K.S.S. / Hammock, B.D. / Morisseau, C. / Madden, D.R.
History
DepositionOct 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: CFTR inhibitory factor
D: CFTR inhibitory factor
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,2088
Polymers136,6554
Non-polymers5534
Water20,8251156
1
C: CFTR inhibitory factor
D: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6044
Polymers68,3272
Non-polymers2762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-9 kcal/mol
Surface area20340 Å2
MethodPISA
2
A: CFTR inhibitory factor
B: CFTR inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6044
Polymers68,3272
Non-polymers2762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-7 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.173, 83.979, 89.169
Angle α, β, γ (deg.)90.00, 100.55, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
CFTR inhibitory factor /


Mass: 34163.715 Da / Num. of mol.: 4 / Mutation: E153Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: PA14_26090 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: A0A0M3KL26, UniProt: A0A0H2ZD27*PLUS
#2: Chemical
ChemComp-FEH / (1R)-1-phenylethane-1,2-diol


Mass: 138.164 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1156 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsFEH is bound form of (R)-Styrene oxide via its C8 atom convalently linked to OD1 atom of ASP ...FEH is bound form of (R)-Styrene oxide via its C8 atom convalently linked to OD1 atom of ASP residue 129 of CIF.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: sodium acetate, pH5 calcium chloride PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→19.806 Å / Num. obs: 194347 / % possible obs: 99.8 % / Redundancy: 4.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.76
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 4.67 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.49 / CC1/2: 0.872 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSOct 15, 2015data reduction
XDSOct 15, 2015data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2
Resolution: 1.5→19.806 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1829 9700 4.99 %
Rwork0.1614 --
obs0.1625 194339 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→19.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 36 1156 10544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069883
X-RAY DIFFRACTIONf_angle_d0.83813453
X-RAY DIFFRACTIONf_dihedral_angle_d14.5895838
X-RAY DIFFRACTIONf_chiral_restr0.0521389
X-RAY DIFFRACTIONf_plane_restr0.0061774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.24294850.23075993X-RAY DIFFRACTION100
1.517-1.53491000000000.22126416X-RAY DIFFRACTION100
1.5349-1.55360.23534850.21356000X-RAY DIFFRACTION100
1.5536-1.57320.23184850.20735950X-RAY DIFFRACTION100
1.5732-1.59391000000000.19726484X-RAY DIFFRACTION100
1.5939-1.61580.23344850.19165953X-RAY DIFFRACTION100
1.6158-1.63880.2144850.18875909X-RAY DIFFRACTION100
1.6388-1.66331000000000.17416472X-RAY DIFFRACTION100
1.6633-1.68930.19084850.16855984X-RAY DIFFRACTION100
1.6893-1.71690.18624850.17146009X-RAY DIFFRACTION100
1.7169-1.74651000000000.16976482X-RAY DIFFRACTION100
1.7465-1.77830.18714850.16785915X-RAY DIFFRACTION100
1.7783-1.81250.20984850.1715978X-RAY DIFFRACTION100
1.8125-1.84941000000000.17026469X-RAY DIFFRACTION100
1.8494-1.88960.20444850.17315994X-RAY DIFFRACTION100
1.8896-1.93350.18774850.16325980X-RAY DIFFRACTION100
1.9335-1.98181000000000.16526440X-RAY DIFFRACTION100
1.9818-2.03540.19264850.15865970X-RAY DIFFRACTION100
2.0354-2.09520.17194850.1615996X-RAY DIFFRACTION100
2.0952-2.16271000000000.15766464X-RAY DIFFRACTION100
2.1627-2.23990.19174850.16016032X-RAY DIFFRACTION100
2.2399-2.32950.18794850.16175981X-RAY DIFFRACTION100
2.3295-2.43531000000000.15916459X-RAY DIFFRACTION100
2.4353-2.56350.17924850.16366015X-RAY DIFFRACTION100
2.5635-2.72370.17424850.16516026X-RAY DIFFRACTION100
2.7237-2.93341000000000.16326509X-RAY DIFFRACTION100
2.9334-3.22750.18524850.16096043X-RAY DIFFRACTION100
3.2275-3.69180.17194850.14746012X-RAY DIFFRACTION100
3.6918-4.64141000000000.13626561X-RAY DIFFRACTION100
4.6414-19.8080.15264850.15336143X-RAY DIFFRACTION100
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)
10.816-0.0048-0.01621.12560.08790.7469-0.005-0.06480.1270.0835-0.01-0.0934-0.08570.02190.01410.10370.0147-0.00110.1013-0.00390.1135.7004-0.096726.9011
21.0548-0.3614-0.05241.35880.24820.62180.02980.029-0.0394-0.0366-0.0026-0.13340.04970.0171-0.02060.08730.02150.01070.09650.00070.077914.5396-38.969815.6863
30.8881-0.00490.07780.9087-0.02060.7043-0.0113-0.1205-0.10450.0980.00360.04960.0881-0.03140.00910.10220.01330.0090.1120.01330.0741-22.0925-31.813627.1034
41.0951-0.4458-0.00441.4595-0.16290.6481-0.01540.01210.1621-0.04970.01130.0353-0.0797-0.01840.00550.08240.0144-0.02290.09510.00030.1305-30.87916.982115.4447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain C and resid 25:317)
2X-RAY DIFFRACTION2(chain D and resid 25:317)
3X-RAY DIFFRACTION3(chain A and resid 25:317)
4X-RAY DIFFRACTION4(chain B and resid 25:317)

+
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