[English] 日本語
Yorodumi
- PDB-4dno: Crystal structure of the CFTR inhibitory factor Cif with the E153... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dno
TitleCrystal structure of the CFTR inhibitory factor Cif with the E153Q mutation adducted with the 1,2-epoxyhexane hydrolysis intermediate
ComponentsPutative hydrolase
KeywordsHYDROLASE / Alpha Beta Hydrolase / Epoxide Hydrolase covalently adducted with the 1 / 2-epoxyhexane hydrolysis intermediate / secreted
Function / homology
Function and homology information


soluble epoxide hydrolase / epoxide hydrolase activity / hydrolase activity / host cell / extracellular region
Similarity search - Function
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
(2R)-hexane-1,2-diol / CFTR inhibitory factor / Putative hydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBahl, C.D. / Patankar, Y.R. / Madden, D.R.
CitationJournal: Biochemistry / Year: 2016
Title: Visualizing the Mechanism of Epoxide Hydrolysis by the Bacterial Virulence Enzyme Cif.
Authors: Bahl, C.D. / Hvorecny, K.L. / Morisseau, C. / Gerber, S.A. / Madden, D.R.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Feb 24, 2016Group: Database references
Revision 1.3Nov 2, 2016Group: Derived calculations / Non-polymer description
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Sep 13, 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 / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative hydrolase
B: Putative hydrolase
C: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,1288
Polymers136,6554
Non-polymers4734
Water17,925995
1
A: Putative hydrolase
B: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5644
Polymers68,3272
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-32 kcal/mol
Surface area20570 Å2
MethodPISA
2
C: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5644
Polymers68,3272
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-33 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.080, 83.663, 89.248
Angle α, β, γ (deg.)90.00, 100.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-617-

HOH

21A-734-

HOH

31C-700-

HOH

41C-704-

HOH

51D-637-

HOH

-
Components

#1: Protein
Putative hydrolase


Mass: 34163.715 Da / Num. of mol.: 4 / Fragment: Cif (UNP Residues 25-319) / Mutation: E153Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: PA14_26090 / Plasmid: pMQ70 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q02P97, UniProt: A0A0H2ZD27*PLUS
#2: Chemical
ChemComp-7FB / (2R)-hexane-1,2-diol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 995 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 14% PEG 8000, 0.125M calcium chloride, 0.1M sodium acetate, 0.01M 1,2-epoxyhexane, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.2006 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 25, 2011 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2006 Å / Relative weight: 1
ReflectionResolution: 1.95→46.01 Å / Num. obs: 88446 / % possible obs: 99.7 % / Redundancy: 4.8 % / Rsym value: 0.099 / Net I/σ(I): 11.68
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.53 / Num. unique all: 24024 / Rsym value: 0.394 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN A OF PDB ENTRY 3KD2

3kd2


Resolution: 1.95→46.008 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 4411 4.99 %thin shells
Rwork0.1734 ---
obs0.1759 88434 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.367 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.9225 Å2-0 Å20.2055 Å2
2---2.9237 Å20 Å2
3---8.8462 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9426 0 28 995 10449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069819
X-RAY DIFFRACTIONf_angle_d1.00613314
X-RAY DIFFRACTIONf_dihedral_angle_d14.1483568
X-RAY DIFFRACTIONf_chiral_restr0.0731364
X-RAY DIFFRACTIONf_plane_restr0.0051752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.30012170.21712660X-RAY DIFFRACTION98
1.9722-1.99541000000000.20992919X-RAY DIFFRACTION99
1.9954-2.01970.26642210.20152678X-RAY DIFFRACTION100
2.0197-2.04530.27622200.18932763X-RAY DIFFRACTION100
2.0453-2.07221000000000.19352907X-RAY DIFFRACTION100
2.0722-2.10060.24412190.18372706X-RAY DIFFRACTION100
2.1006-2.13060.23652210.17342748X-RAY DIFFRACTION100
2.1306-2.16241000000000.16722886X-RAY DIFFRACTION100
2.1624-2.19620.21462200.16262754X-RAY DIFFRACTION100
2.1962-2.23220.20812210.16082744X-RAY DIFFRACTION100
2.2322-2.27071000000000.17162898X-RAY DIFFRACTION100
2.2707-2.31190.25832210.17042720X-RAY DIFFRACTION100
2.3119-2.35640.22182210.16052733X-RAY DIFFRACTION100
2.3564-2.40451000000000.17412972X-RAY DIFFRACTION100
2.4045-2.45680.23442210.17072686X-RAY DIFFRACTION100
2.4568-2.51390.22252210.1732710X-RAY DIFFRACTION100
2.5139-2.57681000000000.17162961X-RAY DIFFRACTION100
2.5768-2.64650.26242210.17352717X-RAY DIFFRACTION100
2.6465-2.72430.22152210.16822742X-RAY DIFFRACTION100
2.7243-2.81221000000000.17082946X-RAY DIFFRACTION100
2.8122-2.91270.24252210.17452728X-RAY DIFFRACTION100
2.9127-3.02930.23032210.18032757X-RAY DIFFRACTION100
3.0293-3.16721000000000.17792920X-RAY DIFFRACTION100
3.1672-3.33410.20872210.1752744X-RAY DIFFRACTION100
3.3341-3.54290.21452210.1732727X-RAY DIFFRACTION100
3.5429-3.81641000000000.16663001X-RAY DIFFRACTION100
3.8164-4.20020.18932210.15062730X-RAY DIFFRACTION100
4.2002-4.80740.17432200.13752746X-RAY DIFFRACTION100
4.8074-6.05471000000000.16313001X-RAY DIFFRACTION100
6.0547-46.02070.26482210.23352819X-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)
10.24410.02650.04910.2767-0.00470.25810.00020.0132-0.05020.0048-0.0084-0.05260.05190.00560.00480.0562-0.00360.00040.0577-0.00630.056322.038212.4459-27.3134
20.08290.02390.01390.05890.01380.0479-0.032-0.01330.08480.02050.035-0.0546-0.0380.00090.0110.0605-0.0257-0.01450.0564-0.01310.113630.847951.4147-15.6035
30.15940.037-0.04020.1460.02840.24320.0227-0.01180.10090.0005-0.02620.0522-0.0558-0.01620.00120.0657-0.00170.0110.0666-0.00040.1018-5.719144.5884-27.2337
40.19370.0754-0.02780.2458-0.07850.16090.0108-0.0257-0.00220.02250.00980.07250.02790.0232-0.00370.0705-0.02520.01010.06890.00390.0625-14.55995.5379-15.7611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:321)
2X-RAY DIFFRACTION2(chain B and resid 25:317)
3X-RAY DIFFRACTION3(chain C and resid 25:321)
4X-RAY DIFFRACTION4(chain D and resid 25:318)

+
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