[English] 日本語
Yorodumi
- PDB-3pi6: Crystal structure of the CFTR inhibitory factor Cif with the H177... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pi6
TitleCrystal structure of the CFTR inhibitory factor Cif with the H177Y mutation
Componentshydrolase
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / epoxide hydrolase / secreted
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
Putative hydrolase / Putative hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBahl, C.D. / Madden, D.R.
CitationJournal: Protein Pept.Lett. / Year: 2012
Title: Pseudomonas aeruginosa Cif defines a distinct class of alpha/beta epoxide hydrolases utilizing a His/Tyr ring-opening pair.
Authors: Bahl, C.D. / Madden, D.R.
History
DepositionNov 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hydrolase
B: hydrolase
C: hydrolase
D: hydrolase


Theoretical massNumber of molelcules
Total (without water)136,7594
Polymers136,7594
Non-polymers00
Water22,4111244
1
A: hydrolase
B: hydrolase


Theoretical massNumber of molelcules
Total (without water)68,3792
Polymers68,3792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-23 kcal/mol
Surface area21000 Å2
MethodPISA
2
C: hydrolase
D: hydrolase


Theoretical massNumber of molelcules
Total (without water)68,3792
Polymers68,3792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-23 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.394, 84.056, 89.325
Angle α, β, γ (deg.)90.00, 100.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-809-

HOH

-
Components

#1: Protein
hydrolase / / CFTR inhibitory factor Cif


Mass: 34189.727 Da / Num. of mol.: 4 / Mutation: H177Y
Source method: isolated from a genetically manipulated source
Details: secreted protein was purified from growth medium / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: cif, PA14_26090 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q02P97, UniProt: A0A0H2ZD27*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1244 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16% PEG 8000, 0.125M CALCIUM CHLORIDE, 0.1M SODIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 11, 2009 / Details: Oxford Danfysik toroidal focusing mirror.
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.5→46.15 Å / Num. obs: 195124 / % possible obs: 99.8 % / Rsym value: 0.051 / Net I/σ(I): 25.7
Reflection shellResolution: 1.5→1.59 Å / Mean I/σ(I) obs: 5.9 / Rsym value: 0.341 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KD2

3kd2


Resolution: 1.5→43.93 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 16.09 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1815 9754 5 %
Rwork0.164 --
obs0.1649 195114 99.79 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.556 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2458 Å20 Å20.0146 Å2
2---0.9027 Å20 Å2
3---2.1485 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9490 0 0 1244 10734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069952
X-RAY DIFFRACTIONf_angle_d1.08213540
X-RAY DIFFRACTIONf_dihedral_angle_d12.5913658
X-RAY DIFFRACTIONf_chiral_restr0.0781393
X-RAY DIFFRACTIONf_plane_restr0.0061779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.55360.25179750.225918236X-RAY DIFFRACTION99
1.5536-1.61580.23149750.193218502X-RAY DIFFRACTION100
1.6158-1.68940.20229760.176418475X-RAY DIFFRACTION100
1.6894-1.77850.19599750.166518536X-RAY DIFFRACTION100
1.7785-1.88990.18029760.154418487X-RAY DIFFRACTION100
1.8899-2.03580.1839750.158618508X-RAY DIFFRACTION100
2.0358-2.24070.18119760.162218615X-RAY DIFFRACTION100
2.2407-2.56490.1789750.159618528X-RAY DIFFRACTION100
2.5649-3.23130.18659760.163318665X-RAY DIFFRACTION100
3.2313-43.9490.15279750.154418808X-RAY DIFFRACTION100
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)
10.38530.00020.05450.370.0760.35880.0022-0.0567-0.03980.042-0.01280.03760.0601-0.02690.00830.0432-0.00070.00950.0440.00910.0257-21.96512.037227.2588
20.6816-0.2805-0.04020.5161-0.08660.3118-0.0090.00520.1013-0.03380.01020.016-0.0496-0.00650.00190.04370.0115-0.01720.0375-0.00350.0711-31.006151.46215.7505
30.32780.00140.07310.42730.02420.4279-0.0044-0.01810.06160.0314-0.0084-0.0526-0.05270.02210.01110.04450.0026-0.00150.0401-0.00440.05335.79444.775727.0021
40.5995-0.13860.02090.50570.10680.24550.01130.0085-0.0334-0.0140.0076-0.07040.02630.0058-0.0150.03970.01670.00540.0464-0.0020.028714.79185.089215.6684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:321)
2X-RAY DIFFRACTION2(chain B and resid 25:320)
3X-RAY DIFFRACTION3(chain C and resid 25:320)
4X-RAY DIFFRACTION4(chain D and resid 25:322)

+
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