[English] 日本語
Yorodumi
- PDB-3oiz: Crystal structure of antisigma-factor antagonist, STAS domain fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oiz
TitleCrystal structure of antisigma-factor antagonist, STAS domain from Rhodobacter sphaeroides
ComponentsAntisigma-factor antagonist, STAS
KeywordsMEMBRANE PROTEIN / PSI-2 / Midwest Center for Structural Genomics / Protein Structure Initiative / MCSG / STAS domain
Function / homology
Function and homology information


: / STAS domain / Transcription Regulator spoIIAA / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Antisigma-factor antagonist, STAS
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsChang, C. / Marshall, N. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of antisigma-factor antagonist, STAS domain from Rhodobacter sphaeroides
Authors: Chang, C. / Marshall, N. / Freeman, L. / Joachimiak, A.
History
DepositionAug 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antisigma-factor antagonist, STAS


Theoretical massNumber of molelcules
Total (without water)11,4421
Polymers11,4421
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.102, 72.102, 36.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Antisigma-factor antagonist, STAS


Mass: 11442.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RHOS4_40800, RSP_4197 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3IUY6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M Calcium acetate, 0.1M MES, 10% iso-propanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 12087 / Num. obs: 12047 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 62.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.9 / Num. unique all: 582 / % possible all: 99.7

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
RESOLVEphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.192 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.101
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 573 4.8 %RANDOM
Rwork0.1597 ---
all0.1623 12008 --
obs0.1623 12008 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.33 Å2 / Biso mean: 30.2107 Å2 / Biso min: 18.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20 Å2
2---1.39 Å20 Å2
3---2.78 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms731 0 0 110 841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022807
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9391095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.42323.25643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84815142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.079159
X-RAY DIFFRACTIONr_chiral_restr0.1090.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02635
X-RAY DIFFRACTIONr_mcbond_it1.6231.5495
X-RAY DIFFRACTIONr_mcangle_it2.7242801
X-RAY DIFFRACTIONr_scbond_it4.2593312
X-RAY DIFFRACTIONr_scangle_it6.7824.5294
X-RAY DIFFRACTIONr_rigid_bond_restr1.8733807
LS refinement shellResolution: 1.648→1.691 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 44 -
Rwork0.205 783 -
all-827 -
obs-827 99.64 %
Refinement TLS params.Method: refined / Origin x: 35.8237 Å / Origin y: 17.1956 Å / Origin z: 16.8824 Å
111213212223313233
T0.0238 Å20.0004 Å2-0.002 Å2-0.0254 Å20.0007 Å2--0.0138 Å2
L0.1607 °2-0.0299 °20.0393 °2-0.1667 °20.0759 °2--0.2801 °2
S-0.0066 Å °-0.0025 Å °0.0095 Å °-0.0054 Å °-0.0008 Å °-0.0054 Å °-0.0141 Å °0.0017 Å °0.0074 Å °

+
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