[English] 日本語
Yorodumi
- PDB-7te2: Crystal Structure of AerR from Rhodobacter capsulatus at 2.25 A. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7te2
TitleCrystal Structure of AerR from Rhodobacter capsulatus at 2.25 A.
ComponentsAerR
KeywordsTRANSCRIPTION / B12 binding / transcription regulator / photosynthesis / gene regulator
Function / homologyB12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / cobalamin binding / metal ion binding / COBALAMIN / HEXANE-1,6-DIOL / B12-binding domain-containing protein
Function and homology information
Biological speciesRhodobacter capsulatus Y262 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsDragnea, V. / Gonzalez-Gutierrez, G. / Bauer, C.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM040941-31 United States
CitationJournal: Microorganisms / Year: 2022
Title: Structural Analyses of CrtJ and Its B 12 -Binding Co-Regulators SAerR and LAerR from the Purple Photosynthetic Bacterium Rhodobacter capsulatus.
Authors: Dragnea, V. / Gonzalez-Gutierrez, G. / Bauer, C.E.
History
DepositionJan 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AerR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3096
Polymers22,7541
Non-polymers1,5555
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.939, 63.939, 182.298
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

-
Components

#1: Protein AerR


Mass: 22754.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus Y262 (bacteria) / Gene: U713_07140 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A829NYX9
#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer detailsThere is split consensus with respect to the geometry in the C19 atom of vitamin B12. Therefore, ...There is split consensus with respect to the geometry in the C19 atom of vitamin B12. Therefore, caution is advised when inspecting this region. Several structures containing B12 in the PDB are modeled using the B12 ligand definition from the CCP4 dictionary, where C19 is planar and has a double bond to N24. However, in high resolution structures (i.e. PDB code 3CI3), C19 atom seems to be tetragonal, which is in agreement with the B12 model in the Cambridge Structural Database (CSD).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: HEPES pH 7.8, NaCl 3.2 M, 1,6-Hexanediol 8%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.25→47.32 Å / Num. obs: 11257 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.024 / Rrim(I) all: 0.107 / Net I/σ(I): 20.6
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 16.8 % / Rmerge(I) obs: 1.804 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1005 / CC1/2: 0.687 / Rpim(I) all: 0.451 / Rrim(I) all: 1.861 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PHENIX1.15_3459refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→47.32 Å / SU ML: 0.2802 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.4215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259 552 5.21 %
Rwork0.2296 10053 -
obs0.2311 10605 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.98 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1542 0 102 77 1721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311701
X-RAY DIFFRACTIONf_angle_d1.27322338
X-RAY DIFFRACTIONf_chiral_restr0.044288
X-RAY DIFFRACTIONf_plane_restr0.0035296
X-RAY DIFFRACTIONf_dihedral_angle_d0.5091090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.480.35641230.29442205X-RAY DIFFRACTION85.9
2.48-2.830.33891170.27972437X-RAY DIFFRACTION93.76
2.83-3.570.26541520.23932606X-RAY DIFFRACTION98.85
3.57-47.320.20381600.1872805X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: 15.8376146567 Å / Origin y: 21.6194081175 Å / Origin z: 97.836297344 Å
111213212223313233
T0.0881916767618 Å20.0158853983796 Å20.0308883685912 Å2-0.218709036737 Å20.0801320492972 Å2--0.126407347139 Å2
L1.44333096875 °2-0.0280551868388 °20.75075372659 °2-2.08493782468 °20.544843386219 °2--1.8394550363 °2
S0.06521970793 Å °0.279484610726 Å °0.0818037312793 Å °-0.0107870743823 Å °-0.110207879062 Å °-0.11418545512 Å °0.00473228936207 Å °0.185143896866 Å °0.0123044657681 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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