[English] 日本語
Yorodumi
- PDB-6uof: 1.2 Angstrom Resolution Crystal Structure of CBS Domains of Trans... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uof
Title1.2 Angstrom Resolution Crystal Structure of CBS Domains of Transcriptional Regulator from Streptococcus pneumoniae
ComponentsTranscriptional regulator containing CBS domains
KeywordsTRANSCRIPTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Transcriptional regulator / CBS domain
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
DRTGG / DRTGG domain / HPr(Ser) kinase/phosphorylase-like, N-terminal domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Thioesterase domain / Thioesterase superfamily / HotDog domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain ...DRTGG / DRTGG domain / HPr(Ser) kinase/phosphorylase-like, N-terminal domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Thioesterase domain / Thioesterase superfamily / HotDog domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.2 Angstrom Resolution Crystal Structure of CBS Domains of Transcriptional Regulator from Streptococcus pneumoniae
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator containing CBS domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9754
Polymers13,8101
Non-polymers1653
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.313, 42.872, 89.098
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Transcriptional regulator containing CBS domains


Mass: 13810.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: spr0991 / Plasmid: pMCSG92 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): DE3 / Variant (production host): magic / References: UniProt: Q8DPV2
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsDuring the crystallization experiment hydrolysis of the protein occurred, probably due to ...During the crystallization experiment hydrolysis of the protein occurred, probably due to contamination with peptidases. The exact length of the protein remaining after hydrolysis is unknown. The presented sequence corresponds to the portion of the protein observed in the electron density.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 34.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 7.12 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3. Screen: Classics II (H1), 0.2M Magnesium chloride, 0.1M TRIS pH 8.5, 25% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 7, 2019 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 33475 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.085 / Rsym value: 0.078 / Χ2: 1.147 / Net I/σ(I): 23.7
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1641 / CC1/2: 0.901 / Rpim(I) all: 0.32 / Rrim(I) all: 0.845 / Rsym value: 0.781 / Χ2: 1.004 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→26.11 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.182 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.045
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 1724 5.2 %RANDOM
Rwork0.1665 ---
obs0.1675 31651 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 59.17 Å2 / Biso mean: 16.808 Å2 / Biso min: 10.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 1.2→26.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 9 173 1131
Biso mean--28.17 28.13 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131067
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171041
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.6581455
X-RAY DIFFRACTIONr_angle_other_deg0.451.5812416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5255143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.692061
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.95115190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.9741513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.021217
X-RAY DIFFRACTIONr_gen_planes_other0.0480.02234
X-RAY DIFFRACTIONr_rigid_bond_restr8.20132108
LS refinement shellResolution: 1.201→1.233 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 126 -
Rwork0.314 2237 -
all-2363 -
obs--96.88 %
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)
11.79420.9941-0.33441.7886-0.64271.13390.00580.1661-0.0441-0.05490.00930.06640.046-0.1104-0.01510.0234-0.00910.00220.2187-0.00660.010322.779920.86217.1152
21.57870.0591-0.26220.71790.42351.85680.0121-0.06930.17770.0485-0.0136-0.0195-0.0725-0.01580.00150.0386-0.0064-0.0050.18080.00190.02332.794231.764210.4295
30.94670.874-0.21471.32310.09660.72890.0529-0.0723-0.0661-0.011-0.0861-0.1039-0.02060.04820.03320.0449-0.0023-0.01460.24760.00840.060237.341925.775410.8288
40.3253-0.3282-0.35560.8782-0.7143.34-0.02860.0407-0.05510.03080.03510.02050.0699-0.1032-0.00650.0384-0.0142-0.00380.1902-0.00030.037226.677116.514312.6299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A185 - 204
2X-RAY DIFFRACTION2A205 - 239
3X-RAY DIFFRACTION3A240 - 266
4X-RAY DIFFRACTION4A267 - 303

+
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