[English] 日本語
Yorodumi
- PDB-5hkb: Crystal structure of the CFTR inhibitory factor Cif bound to the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hkb
TitleCrystal structure of the CFTR inhibitory factor Cif bound to the inhibitor KB2115
ComponentsCFTR Inhibitory Factor (Cif)
KeywordsHydrolase/Hydrolase inhibitor / Bacterial Epoxide Hydrolase / Inhibitor / Hydrolase-Hydrolase inhibitor complex
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
KB2115 / ACETATE ION / Putative hydrolase / CFTR inhibitory factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHvorecny, K.L. / Madden, D.R.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Rational Design of Potent and Selective Inhibitors of an Epoxide Hydrolase Virulence Factor from Pseudomonas aeruginosa.
Authors: Kitamura, S. / Hvorecny, K.L. / Niu, J. / Hammock, B.D. / Madden, D.R. / Morisseau, C.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CFTR Inhibitory Factor (Cif)
B: CFTR Inhibitory Factor (Cif)
C: CFTR Inhibitory Factor (Cif)
D: CFTR Inhibitory Factor (Cif)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,84412
Polymers136,6594
Non-polymers2,1858
Water25,4551413
1
A: CFTR Inhibitory Factor (Cif)
B: CFTR Inhibitory Factor (Cif)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4226
Polymers68,3292
Non-polymers1,0924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-28 kcal/mol
Surface area21040 Å2
MethodPISA
2
C: CFTR Inhibitory Factor (Cif)
D: CFTR Inhibitory Factor (Cif)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4226
Polymers68,3292
Non-polymers1,0924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-27 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.168, 169.494, 175.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-720-

HOH

21D-855-

HOH

-
Components

#1: Protein
CFTR Inhibitory Factor (Cif)


Mass: 34164.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Gene: PA14_26090 / Plasmid: pDPM73 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: A0A0M3KL26, UniProt: A0A0H2ZD27*PLUS
#2: Chemical
ChemComp-64L / KB2115 / 3-({3,5-dibromo-4-[4-hydroxy-3-(propan-2-yl)phenoxy]phenyl}amino)-3-oxopropanoic acid


Mass: 487.139 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H17Br2NO5
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1413 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8000, Calcium Chloride, Sodium Acetate, Dimethylsulfoxide

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→19.921 Å / Num. obs: 150068 / % possible obs: 99.99 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 21.76
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 7.22 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
XDSJanuary 10, 2014data reduction
XSCALEJanuary 10, 2014data scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KB2

3kb2


Resolution: 1.65→19.921 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 7518 5.01 %
Rwork0.1895 --
obs0.1908 150014 99.95 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.331 Å2 / ksol: 0.424 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3607 Å2-0 Å20 Å2
2---1.4636 Å20 Å2
3---3.8243 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9492 0 120 1413 11025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710041
X-RAY DIFFRACTIONf_angle_d1.16113661
X-RAY DIFFRACTIONf_dihedral_angle_d13.7413693
X-RAY DIFFRACTIONf_chiral_restr0.0791392
X-RAY DIFFRACTIONf_plane_restr0.0061801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66870.24533760.23584558X-RAY DIFFRACTION100
1.6687-1.68841000000000.21985009X-RAY DIFFRACTION100
1.6884-1.70890.26723760.22484541X-RAY DIFFRACTION100
1.7089-1.73060.26793760.22424589X-RAY DIFFRACTION100
1.7306-1.75331000000000.21464998X-RAY DIFFRACTION100
1.7533-1.77730.26333760.21194529X-RAY DIFFRACTION100
1.7773-1.80270.2453760.20234596X-RAY DIFFRACTION100
1.8027-1.82961000000000.1995016X-RAY DIFFRACTION100
1.8296-1.85820.22853760.1944574X-RAY DIFFRACTION100
1.8582-1.88860.2313760.18794594X-RAY DIFFRACTION100
1.8886-1.92111000000000.20014937X-RAY DIFFRACTION100
1.9211-1.9560.22463760.18774601X-RAY DIFFRACTION100
1.956-1.99360.22423760.18794604X-RAY DIFFRACTION100
1.9936-2.03431000000000.18914973X-RAY DIFFRACTION100
2.0343-2.07850.21573750.18794615X-RAY DIFFRACTION100
2.0785-2.12680.19713750.18914578X-RAY DIFFRACTION100
2.1268-2.17991000000000.18784997X-RAY DIFFRACTION100
2.1799-2.23880.21753760.18764622X-RAY DIFFRACTION100
2.2388-2.30450.22443760.19124624X-RAY DIFFRACTION100
2.3045-2.37881000000000.17984991X-RAY DIFFRACTION100
2.3788-2.46370.19123760.18244616X-RAY DIFFRACTION100
2.4637-2.56210.21063760.18834652X-RAY DIFFRACTION100
2.5621-2.67851000000000.18094983X-RAY DIFFRACTION100
2.6785-2.81930.1973760.17434653X-RAY DIFFRACTION100
2.8193-2.99540.18583760.18014639X-RAY DIFFRACTION100
2.9954-3.22581000000000.17985064X-RAY DIFFRACTION100
3.2258-3.54880.19223760.17184673X-RAY DIFFRACTION100
3.5488-4.05850.18883760.17154698X-RAY DIFFRACTION100
4.0585-5.09911000000000.16255102X-RAY DIFFRACTION100
5.0991-19.92290.25113760.2544870X-RAY DIFFRACTION99
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)
10.4949-0.03130.0250.46770.14860.5805-0.0107-0.0207-0.02550.0460.0118-0.03860.03180.05450.00290.0387-0.0084-0.00070.03150.01320.02416.601-22.0094202.8195
20.84190.34910.02640.9572-0.08280.350.00310.03760.0124-0.0283-0.00530.1290.0126-0.04070.0020.0326-0.01660.00410.0391-0.0120.0419-23.157-31.3901191.1672
30.6142-0.15340.00140.50660.02960.5222-0.0181-0.01860.05360.03070.00530.0531-0.0159-0.0499-0.00270.0263-0.01010.01310.03110.00560.0353-16.49845.4778202.7093
40.68690.3374-0.10740.89580.18260.382-0.00490.00570.1088-0.02850.0294-0.0434-0.01130.022-0.00510.0304-0.02080.01290.02390.0366-0.006423.338114.9332191.1087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:321)
2X-RAY DIFFRACTION2(chain B and resid 25:321)
3X-RAY DIFFRACTION3(chain C and resid 25:321)
4X-RAY DIFFRACTION4(chain D and resid 25:321)

+
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