[English] 日本語
Yorodumi
- PDB-4mo7: Crystal structure of superantigen PfiT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mo7
TitleCrystal structure of superantigen PfiT
ComponentsTranscriptional regulator I2
KeywordsTRANSCRIPTION / TetR / Superantigen
Function / homologyTetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / BETA-MERCAPTOETHANOL / :
Function and homology information
Biological speciesPseudomonas fluorescens A506 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.701 Å
AuthorsLiu, L.H. / Chen, H. / Li, H.M.
CitationJournal: Plos Pathog. / Year: 2013
Title: Pfit is a structurally novel Crohn's disease-associated superantigen.
Authors: Liu, L. / Chen, H. / Brecher, M.B. / Li, Z. / Wei, B. / Nandi, B. / Zhang, J. / Ling, H. / Winslow, G. / Braun, J. / Li, H.
History
DepositionSep 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator I2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7403
Polymers23,6371
Non-polymers1022
Water2,000111
1
A: Transcriptional regulator I2
hetero molecules

A: Transcriptional regulator I2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4796
Polymers47,2742
Non-polymers2054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_857-x+3,y,-z+21
Buried area2390 Å2
ΔGint-18 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.226, 93.661, 53.557
Angle α, β, γ (deg.)90.00, 109.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

MG

21A-357-

HOH

31A-384-

HOH

41A-388-

HOH

-
Components

#1: Protein Transcriptional regulator I2


Mass: 23637.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens A506 (bacteria)
Gene: pfiT, PflA506_3695 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I2BPL4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.86 Å3/Da / Density % sol: 33.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 4-8% PEG 3350, 0.1 M Tris, 0.2 M ammonium acetate, 5 mM MgCl2, 5 mM DTT, 5% isopropanol, and 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.04023 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2005
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04023 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 57293 / Num. obs: 18843 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 30.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1851 / Rsym value: 0.556 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.refine: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: SAD / Resolution: 1.701→25.192 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 938 4.98 %RANDOM
Rwork0.1886 ---
obs0.1908 18840 99.32 %-
all-18840 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.804 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3004 Å20 Å2-1.3445 Å2
2---0.3717 Å2-0 Å2
3---1.6721 Å2
Refinement stepCycle: LAST / Resolution: 1.701→25.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 5 111 1598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161568
X-RAY DIFFRACTIONf_angle_d1.5722121
X-RAY DIFFRACTIONf_dihedral_angle_d15.408581
X-RAY DIFFRACTIONf_chiral_restr0.105239
X-RAY DIFFRACTIONf_plane_restr0.006273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7006-1.79020.38511340.30542505X-RAY DIFFRACTION97
1.7902-1.90240.34421300.24412545X-RAY DIFFRACTION100
1.9024-2.04920.2451370.20842559X-RAY DIFFRACTION100
2.0492-2.25530.23671300.18112565X-RAY DIFFRACTION100
2.2553-2.58130.23041380.17052558X-RAY DIFFRACTION100
2.5813-3.25110.2071380.17312580X-RAY DIFFRACTION100
3.2511-25.19430.2141310.18062590X-RAY DIFFRACTION99

+
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