[English] 日本語
Yorodumi
- PDB-4iqn: Crystal structure of uncharacterized protein from Salmonella ente... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iqn
TitleCrystal structure of uncharacterized protein from Salmonella enterica subsp. enterica serovar typhimurium str. 14028s
Components(Putative cytoplasmic ...) x 3
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-BIOLOGY / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS / PROGRAM FOR THE CHARACTERIZATION OF SECRETED EFFECTOR PROTEINS / PCSEP / reductive METHYLATION
Function / homologyDomain of unknown function (DUF5066) / Protein of unknown function DUF5066 / Domain of unknown function (DUF5066) / SMI1/KNR4-like / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Putative cytoplasmic protein / Putative cytoplasmic protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsChang, C. / Hatzos-Skintges, C. / Adkins, J.N. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein from salmonella enterica subsp. enterica serovar typhimurium str. 14028s
Authors: Chang, C. / Hatzos-Skintges, C. / Adkins, J.N. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionJan 11, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 23, 2013ID: 4HG1
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative cytoplasmic protein
B: Putative cytoplasmic protein
C: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2845
Polymers78,9833
Non-polymers3002
Water9,836546
1
A: Putative cytoplasmic protein


Theoretical massNumber of molelcules
Total (without water)26,3051
Polymers26,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4662
Polymers26,3591
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5132
Polymers26,3181
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.138, 95.477, 69.897
Angle α, β, γ (deg.)90.00, 109.66, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Putative cytoplasmic ... , 3 types, 3 molecules ABC

#1: Protein Putative cytoplasmic protein


Mass: 26305.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: 14028s / SGSC 2262 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: D0ZRV8, UniProt: A0A0F6B4U8*PLUS
#2: Protein Putative cytoplasmic protein


Mass: 26359.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: 14028s / SGSC 2262 / Production host: Escherichia coli (E. coli) / References: UniProt: D0ZRV8, UniProt: A0A0F6B4U8*PLUS
#3: Protein Putative cytoplasmic protein


Mass: 26318.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: 14028s / SGSC 2262 / Production host: Escherichia coli (E. coli) / References: UniProt: D0ZRV8, UniProt: A0A0F6B4U8*PLUS

-
Non-polymers , 3 types, 548 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2012
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 79623 / Num. obs: 76983 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 41.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.71 / Num. unique all: 3773 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
SBC-CollectCOLLECTdata collection
MLPHAREphasing
DMmodel building
SHELXDEphasing
RESOLVEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→31.13 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.131 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.102
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19568 3848 5 %RANDOM
Rwork0.13496 ---
all0.13799 72717 --
obs0.13799 72717 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.887 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å2-0 Å2-1.44 Å2
2--2.96 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.75→31.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5382 0 20 546 5948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195819
X-RAY DIFFRACTIONr_bond_other_d0.0010.025419
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9957940
X-RAY DIFFRACTIONr_angle_other_deg0.839312536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.395723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70525.292308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46715905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8751538
X-RAY DIFFRACTIONr_chiral_restr0.0940.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216723
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021271
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr4.41311238
X-RAY DIFFRACTIONr_sphericity_free27.2575141
X-RAY DIFFRACTIONr_sphericity_bonded16.303511504
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 269 -
Rwork0.175 5052 -
obs-5229 93.14 %

+
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