[English] 日本語
Yorodumi
- PDB-4glq: Crystal Structure of the blue-light absorbing form of the Thermos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4glq
TitleCrystal Structure of the blue-light absorbing form of the Thermosynechococcus elongatus PixJ GAF-domain
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / chromophore / phytochrome / cyanobacteriochrome / phycoviolobilin / bilin / bili-protein / cation-pi interaction / GAF domain / photoreceptor / phycoviolobilin adduct
Function / homology
Function and homology information


chemotaxis / lysozyme activity / signal transduction / metal ion binding / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / GAF domain / HAMP domain ...Double Cache domain 1 / Cache domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / GAF domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phycoviolobilin, blue light-absorbing form / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.772 Å
AuthorsBurgie, E.S. / Walker, J.M. / Phillips Jr., G.N. / Vierstra, R.D.
CitationJournal: Structure / Year: 2013
Title: A Photo-Labile Thioether Linkage to Phycoviolobilin Provides the Foundation for the Blue/Green Photocycles in DXCF-Cyanobacteriochromes.
Authors: Burgie, E.S. / Walker, J.M. / Phillips Jr., G.N. / Vierstra, R.D.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3May 15, 2013Group: Non-polymer description
Revision 1.4Nov 15, 2017Group: Database references / Refinement description / Structure summary
Category: audit_author / citation_author / software
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 23, 2020Group: Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.name / _chem_comp.pdbx_synonyms ..._audit_author.name / _chem_comp.pdbx_synonyms / _citation_author.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Mar 13, 2024Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1892
Polymers19,5981
Non-polymers5911
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Methyl-accepting chemotaxis protein
hetero molecules

A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3784
Polymers39,1962
Non-polymers1,1812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_467y-1,x+1,-z+21
Buried area1900 Å2
ΔGint-11 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.040, 47.040, 125.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Methyl-accepting chemotaxis protein


Mass: 19598.188 Da / Num. of mol.: 1 / Mutation: C555A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: tll0569 / Plasmid: pBAD-Myc-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q8DLC7
#2: Chemical ChemComp-VRB / Phycoviolobilin, blue light-absorbing form / 3-[5-[(3-ethyl-4-methyl-5-oxidanylidene-1,2-dihydropyrrol-2-yl)methyl]-2-[[5-[(Z)-(4-ethyl-3-methyl-5-oxidanylidene-pyr rol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid


Mass: 590.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H42N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 50 mM NaCl, 0.3 mM tris(2-carboxyethyl)phosphine, 10 mM HEPES-NaOH (pH 7.8), 25% polyethylene glycol 3350, 200 mM sodium chloride, 40 mM glycine, 100 mM BIS-TRIS-HCl, (pH 5.5), vapor ...Details: 50 mM NaCl, 0.3 mM tris(2-carboxyethyl)phosphine, 10 mM HEPES-NaOH (pH 7.8), 25% polyethylene glycol 3350, 200 mM sodium chloride, 40 mM glycine, 100 mM BIS-TRIS-HCl, (pH 5.5), vapor diffusion, sitting drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97895 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 14559 / Num. obs: 14530 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.069 / Χ2: 1.081 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.77-1.89.50.3236990.709198.5
1.8-1.839.90.2926890.771199.3
1.83-1.879.70.2397150.776199.4
1.87-1.919.80.2146930.826199.7
1.91-1.959.70.1837300.902199.9
1.95-1.99100.1546820.971199.3
1.99-2.049.70.1367160.958199.6
2.04-2.110.10.1137141.0041100
2.1-2.169.90.1067041.057199.9
2.16-2.239.90.0997271.0381100
2.23-2.31100.0977051.0671100
2.31-2.4100.0927181.187199.9
2.4-2.5110.10.0867251.19199.7
2.51-2.6410.10.0787261.151100
2.64-2.8110.10.0677281.1061100
2.81-3.0310.40.0647361.1641100
3.03-3.3310.50.0637421.5351100
3.33-3.8110.40.0577471.5231100
3.81-4.810.10.0467801.1531100
4.8-509.20.0528541.3261100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.77 Å44.07 Å
Translation1.77 Å44.07 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SyB Cph1-GAF domain

Resolution: 1.772→44.068 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.11 / σ(F): 0 / Phase error: 17.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 1437 10.02 %random
Rwork0.1546 ---
all0.159 14498 --
obs0.159 14336 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.57 Å2 / Biso mean: 34.2812 Å2 / Biso min: 22.18 Å2
Refinement stepCycle: LAST / Resolution: 1.772→44.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 43 137 1381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071349
X-RAY DIFFRACTIONf_angle_d1.2641851
X-RAY DIFFRACTIONf_chiral_restr0.083200
X-RAY DIFFRACTIONf_plane_restr0.005244
X-RAY DIFFRACTIONf_dihedral_angle_d17.122530
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7718-1.83520.22591360.16461206134296
1.8352-1.90860.21881360.15871227136397
1.9086-1.99550.18761400.1461257139799
1.9955-2.10070.20781430.14561270141399
2.1007-2.23230.19051410.141312821423100
2.2323-2.40470.22031420.156612701412100
2.4047-2.64660.20911440.170712991443100
2.6466-3.02950.19861460.1713121458100
3.0295-3.81660.1911480.142113331481100
3.8166-44.08120.19161610.155914431604100
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)
17.8573.95832.3369.01731.57393.4624-0.31780.46780.4159-0.15430.2222-0.4498-0.30790.38090.03560.27530.01610.02220.3010.00960.264326.1684.2099126.2912
21.55160.51671.381.83121.37495.155-0.00920.06060.16490.03720.0283-0.0772-0.0768-0.0031-0.0410.23490.01220.00290.23070.0070.275319.370387.3786135.7801
31.41290.15942.43951.41570.83576.3018-0.04430.12220.0843-0.19240.10190.0584-0.4454-0.2105-0.06390.27350.0088-0.00980.28260.04440.28213.10691.5712131.2396
41.95880.19231.81321.45981.23372.44120.1079-0.0826-0.07220.1202-0.03290.02080.1811-0.0428-0.09020.2956-0.01170.00940.25290.03110.265812.916777.5165143.5422
50.0074-0.08430.09035.6059-5.6325.6599-0.0706-0.20860.53090.32580.07720.1139-0.8086-0.8152-0.10260.33710.0585-0.0030.37770.00150.40234.39187.9134140.5653
64.81822.7271.46812.95311.01393.24040.07480.22920.02710.02060.03640.04780.13320.0884-0.08840.21940.01590.0240.20220.00450.2114.789778.9892134.2904
72.8181-0.1463-1.40371.55920.70162.3222-0.0309-0.09890.0335-0.02470.109-0.10220.0840.2444-0.08390.24810.0222-0.01180.25190.0120.22223.172575.3256133.234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 436:455 )A436 - 455
2X-RAY DIFFRACTION2( CHAIN A AND RESID 456:478 )A456 - 478
3X-RAY DIFFRACTION3( CHAIN A AND RESID 479:493 )A479 - 493
4X-RAY DIFFRACTION4( CHAIN A AND RESID 494:520 )A494 - 520
5X-RAY DIFFRACTION5( CHAIN A AND RESID 521:530 )A521 - 530
6X-RAY DIFFRACTION6( CHAIN A AND RESID 531:562 )A531 - 562
7X-RAY DIFFRACTION7( CHAIN A AND ( RESID 563:584 OR RESID 1000:1000 ) )A563 - 584
8X-RAY DIFFRACTION7( CHAIN A AND ( RESID 563:584 OR RESID 1000:1000 ) )A1000

+
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