[English] 日本語
Yorodumi
- PDB-8h17: Crystal structure of the Globin domain of Thermosynechococcus elo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h17
TitleCrystal structure of the Globin domain of Thermosynechococcus elongatus BP-1
ComponentsTlr1989 protein
KeywordsOXYGEN BINDING / Thermosynechococcus vestitus BP-1 / Haemoglobin / Imidazole / Penta-cordinated heme / Heme binding / Iron / Thermophile / Cyanobacteria / Synechococcus
Function / homologyGlobin-sensor domain / Protoglobin / Globin/Protoglobin / Globin-like superfamily / oxygen binding / heme binding / PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Tlr1989 protein
Function and homology information
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMathur, S. / Yadav, S.K. / Pal, K.R. / Kundu, S.
Funding support India, 5items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
Department of Science & Technology (DST, India) India
Delhi University, IoE India
Defense research development organization India
University Grants Commission India
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: A novel single sensor hemoglobin domain from the thermophilic cyanobacteria Thermosynechococcus elongatus BP-1 exhibits higher pH but lower thermal stability compared to globins from mesophilic organisms.
Authors: Mathur, S. / Yadav, S.K. / Yadav, K. / Bhatt, S. / Kundu, S.
History
DepositionSep 30, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tlr1989 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5303
Polymers22,8441
Non-polymers6862
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-17 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.041, 54.041, 112.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Tlr1989 protein


Mass: 22844.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus BP-1 (bacteria)
Gene: tlr1989 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8DHH0
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 35 % / Description: Red colour, Thick square plate
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.5 M Ammonium sulfate, 0.1 M MES 0.02 M Cobalt chloride hexahydrate 10% Glycerol
PH range: 6-7

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.15→35 Å / Num. obs: 9714 / % possible obs: 99.7 % / Redundancy: 23.9 % / CC1/2: 0.99 / Net I/σ(I): 65.5
Reflection shellResolution: 2.15→2.23 Å / Num. unique obs: 932 / CC1/2: 0.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alfa fold

Resolution: 2.15→22.23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.457 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22292 461 4.8 %RANDOM
Rwork0.1762 ---
obs0.17855 9193 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.414 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2---1.28 Å20 Å2
3---2.56 Å2
Refinement stepCycle: 1 / Resolution: 2.15→22.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 48 25 1324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0121324
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161196
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.6921802
X-RAY DIFFRACTIONr_angle_other_deg1.0671.5882762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0595154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.6631010
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15610217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021523
X-RAY DIFFRACTIONr_gen_planes_other0.030.02291
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_it2.7744.977622
X-RAY DIFFRACTIONr_mcbond_other2.7734.977622
X-RAY DIFFRACTIONr_mcangle_it3.9977.427774
X-RAY DIFFRACTIONr_mcangle_other3.9957.437775
X-RAY DIFFRACTIONr_scbond_it3.6285.346702
X-RAY DIFFRACTIONr_scbond_other3.6225.345700
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6157.8551028
X-RAY DIFFRACTIONr_long_range_B_refined7.37365.7691633
X-RAY DIFFRACTIONr_long_range_B_other7.37565.7331631
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.203 Å
RfactorNum. reflection% reflection
Rfree0.238 27 -
Rwork0.221 655 -
obs--98.55 %
Refinement TLS params.Method: refined / Origin x: 1.3188 Å / Origin y: -2.1972 Å / Origin z: 17.6575 Å
111213212223313233
T0.0611 Å20.007 Å2-0.0008 Å2-0.1022 Å20.0047 Å2--0.0086 Å2
L1.1733 °20.1734 °2-0.1155 °2-0.8271 °20.3465 °2--0.3753 °2
S-0.0551 Å °0.2141 Å °-0.0417 Å °-0.1019 Å °0.0701 Å °-0.0241 Å °-0.1088 Å °-0.0586 Å °-0.015 Å °

+
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