[English] 日本語
Yorodumi
- PDB-5o3r: Carbon regulatory PII-like protein SbtB from Synechocystis sp. 68... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o3r
TitleCarbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with AMP
ComponentsMembrane-associated protein slr1513
KeywordsSIGNALING PROTEIN / SbtB / Carbon sensing / PII-like / cyanobacteria
Function / homology
Function and homology information


regulation of nitrogen utilization / plasma membrane-derived thylakoid membrane / enzyme regulator activity
Similarity search - Function
Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / BICARBONATE ION / Membrane-associated protein slr1513
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSelim, K.A. / Forchhammer, K. / Albrecht, R. / Hartmann, M.D.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: PII-like signaling protein SbtB links cAMP sensing with cyanobacterial inorganic carbon response.
Authors: Selim, K.A. / Haase, F. / Hartmann, M.D. / Hagemann, M. / Forchhammer, K.
History
DepositionMay 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Membrane-associated protein slr1513
B: Membrane-associated protein slr1513
C: Membrane-associated protein slr1513
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7697
Polymers39,6663
Non-polymers1,1034
Water2,108117
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-40 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.425, 64.425, 80.737
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein Membrane-associated protein slr1513 / SbtB protein


Mass: 13222.110 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: slr1513 / Plasmid: pASK-IBA-3C / Production host: Escherichia coli (E. coli) / References: UniProt: P73954
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: Protein solution containing 19 mg/ml SbtB in 50 mM Tris.HCl (pH 8.0), 250 mM NaCl, 3mM AMP mixed 1:1 with reservoir solution of Molecular Dimensions Morpheus screen condition A2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→32.7 Å / Num. obs: 29560 / % possible obs: 99.9 % / Redundancy: 8.22 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.22 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 4763 / CC1/2: 0.79 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O3P

5o3p


Resolution: 1.9→32.7 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.159 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20686 1479 5 %RANDOM
Rwork0.17653 ---
obs0.17809 28081 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.489 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.28 Å2-0 Å2
2--0.55 Å2-0 Å2
3----1.8 Å2
Refinement stepCycle: 1 / Resolution: 1.9→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 73 117 2449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192436
X-RAY DIFFRACTIONr_bond_other_d0.0010.022335
X-RAY DIFFRACTIONr_angle_refined_deg1.7412.0183301
X-RAY DIFFRACTIONr_angle_other_deg0.78335408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.34425.28189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34215432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.842156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022634
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
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_it2.1663.2671195
X-RAY DIFFRACTIONr_mcbond_other2.1563.2651194
X-RAY DIFFRACTIONr_mcangle_it2.9444.8781487
X-RAY DIFFRACTIONr_mcangle_other2.9454.8811488
X-RAY DIFFRACTIONr_scbond_it3.4393.6971241
X-RAY DIFFRACTIONr_scbond_other3.4323.6921239
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8985.3951808
X-RAY DIFFRACTIONr_long_range_B_refined7.46327.6972749
X-RAY DIFFRACTIONr_long_range_B_other7.40127.4232720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 108 -
Rwork0.309 2079 -
obs--98.96 %
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)
13.84260.6602-0.42625.09020.26313.12710.04320.11650.0615-0.241-0.01940.3894-0.2075-0.4278-0.02380.08480.0886-0.03330.1194-0.01420.0535-14.663122.7515-1.8634
23.3441-1.14980.02133.6004-0.94122.84090.0307-0.1412-0.00510.12930.07910.262-0.1436-0.2187-0.10980.02820.00280.00390.06180.01090.0262-6.59918.49057.5927
32.2454-0.1957-0.17193.5272-1.94545.44080.0527-0.1413-0.02910.0556-0.0414-0.2529-0.17620.3057-0.01130.062-0.02790.00360.0301-0.00590.04225.310618.028-4.2973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 200
2X-RAY DIFFRACTION2B2 - 200
3X-RAY DIFFRACTION3C2 - 201

+
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