[English] 日本語
Yorodumi
- PDB-8j2y: Acidimicrobiaceae bacterium photocobilins protein, dark state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8j2y
TitleAcidimicrobiaceae bacterium photocobilins protein, dark state
ComponentsGGDEF domain-containing protein
KeywordsUNKNOWN FUNCTION / cobalamin binding / biliverdin binding / B12-dependent photoreceptor protein / photocobilins
Function / homology
Function and homology information


cobalamin binding / metal ion binding
Similarity search - Function
Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. ...Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / GGDEF domain-containing protein
Similarity search - Component
Biological speciesAcidimicrobiaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, S. / Poddar, H. / Levy, W.C. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/S030336/1 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Photocobilins integrate B12 and bilin photochemistry for enzyme control.
Authors: Zhang, S. / Jeffreys, L.N. / Poddar, H. / Yu, Y. / Liu, C. / Patel, K. / Johannissen, L.O. / Zhu, L. / Cliff, M.J. / Yan, C. / Schiro, G. / Weik, M. / Sakuma, M. / Levy, C.W. / Leys, D. / ...Authors: Zhang, S. / Jeffreys, L.N. / Poddar, H. / Yu, Y. / Liu, C. / Patel, K. / Johannissen, L.O. / Zhu, L. / Cliff, M.J. / Yan, C. / Schiro, G. / Weik, M. / Sakuma, M. / Levy, C.W. / Leys, D. / Heyes, D.J. / Scrutton, N.S.
History
DepositionApr 15, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GGDEF domain-containing protein
B: GGDEF domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0999
Polymers74,7132
Non-polymers3,3857
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-5 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.773, 125.836, 124.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-539-

HOH

21B-546-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein GGDEF domain-containing protein


Mass: 37356.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidimicrobiaceae bacterium (bacteria) / Gene: DCS55_04760 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A349B205

-
Non-polymers , 5 types, 135 molecules

#2: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 8% PEG 20,000, 8% PEG 550 MME, 0.1M Sodium acetate pH5.5, 0.2M Potassium thiocyanate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→44.31 Å / Num. obs: 38287 / % possible obs: 99.86 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.1766 / Net I/σ(I): 6.95
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.9439 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 3775 / % possible all: 99.79

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DIALSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.31 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.947 / SU B: 20.306 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23664 1996 5.2 %RANDOM
Rwork0.20935 ---
obs0.21085 36286 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---2.59 Å2-0 Å2
3---2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4874 0 231 128 5233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0165251
X-RAY DIFFRACTIONr_bond_other_d0.0030.0154811
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.8417233
X-RAY DIFFRACTIONr_angle_other_deg0.5351.60611107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8195.36709
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65610729
X-RAY DIFFRACTIONr_chiral_restr0.0880.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026179
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021063
X-RAY DIFFRACTIONr_mcbond_it1.6361.8572625
X-RAY DIFFRACTIONr_mcbond_other1.6241.8552623
X-RAY DIFFRACTIONr_mcangle_it2.6852.7693272
X-RAY DIFFRACTIONr_mcangle_other2.6852.773273
X-RAY DIFFRACTIONr_scbond_it1.7111.9642626
X-RAY DIFFRACTIONr_scbond_other1.6911.9642626
X-RAY DIFFRACTIONr_scangle_other2.7082.8853957
X-RAY DIFFRACTIONr_long_range_B_refined6.26724.2865877
X-RAY DIFFRACTIONr_long_range_B_other6.26924.1755857
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 161 -
Rwork0.314 2612 -
obs--99.96 %
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)
13.17921.1620.43152.21110.1743.225-0.16330.33650.1342-0.26910.0010.1853-0.187-0.19340.16230.2918-0.0104-0.04970.5695-0.03090.0254-23.971-33.2918.653
22.31770.2601-0.15842.01870.72932.30210.0653-0.07740.28740.1305-0.1430.0642-0.2957-0.39970.07770.3390.0288-0.02310.6838-0.02540.041-22.045-22.88231.855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 403
2X-RAY DIFFRACTION2B2 - 402

+
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