[English] 日本語
Yorodumi
- PDB-8tls: Crystal structure of Shewanella benthica Group 1 truncated hemogl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tls
TitleCrystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S Y108A variant
ComponentsGroup 1 truncated hemoglobin
KeywordsHEME BINDING PROTEIN / GLOBIN / 2/2 HEMOGLOBIN / UNKNOWN FUNCTION / PSYCHROPIEZOPHILE
Function / homology
Function and homology information


oxygen transport / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin, bacterial-like, conserved site / Protozoan/cyanobacterial globins signature. / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globin-like superfamily
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Group 1 truncated hemoglobin
Similarity search - Component
Biological speciesShewanella benthica KT99 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 Å
AuthorsSchultz, T.D. / Martinez, J.E. / Siegler, M.A. / Schlessman, J.L. / Lecomte, J.T.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1330488 United States
National Science Foundation (NSF, United States)CHE-2003950 United States
National Science Foundation (NSF, United States)GRFP-1746891 United States
CitationJournal: To Be Published
Title: Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S Y108A variant
Authors: Schultz, T.D. / Martinez, J.E. / Siegler, M.A. / Schlessman, J.L. / Lecomte, J.T.J.
History
DepositionJul 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Group 1 truncated hemoglobin
B: Group 1 truncated hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7786
Polymers25,4932
Non-polymers1,2854
Water5,531307
1
A: Group 1 truncated hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3893
Polymers12,7461
Non-polymers6432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Group 1 truncated hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3893
Polymers12,7461
Non-polymers6432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.718, 66.718, 125.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

-
Components

#1: Protein Group 1 truncated hemoglobin


Mass: 12746.330 Da / Num. of mol.: 2 / Mutation: C51S, C71S, Y108A
Source method: isolated from a genetically manipulated source
Details: First residue of reference sequence A9DF82 (Met) is cleaved by E. coli; first residue of sample (Ser) is numbered 2.
Source: (gene. exp.) Shewanella benthica KT99 (bacteria) / Strain: KT99 / Gene: KT99_16901 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9DF82
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CN
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 27% PEG MME 2000, 100 mM Bis-Tris pH 5.1, 10 mM KCN, Excluded from light
PH range: 5.1-6.0 / Temp details: Room Temp

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 29, 2022 / Details: NULL
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→24.28 Å / Num. obs: 59860 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.063 / Net I/σ(I): 24.07
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 4.08 / Num. unique obs: 5978 / Rsym value: 0.221 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(dev_4788: ???)refinement
CrysalisPro1.171.42.49data scaling
PHENIXdev-4788-000phasing
CrysalisPro1.171.42.49data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.7→21.9 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 20.83 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2139 1995 6.27 %
Rwork0.1891 --
obs0.1907 31799 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 90 307 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082004
X-RAY DIFFRACTIONf_angle_d1.0742739
X-RAY DIFFRACTIONf_dihedral_angle_d9.767320
X-RAY DIFFRACTIONf_chiral_restr0.053288
X-RAY DIFFRACTIONf_plane_restr0.008351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.28221400.21192085X-RAY DIFFRACTION100
1.74-1.790.20761400.18812085X-RAY DIFFRACTION100
1.79-1.840.24741420.19392110X-RAY DIFFRACTION100
1.84-1.90.25161380.2292084X-RAY DIFFRACTION100
1.9-1.970.26521410.22642106X-RAY DIFFRACTION100
1.97-2.050.23211400.19582090X-RAY DIFFRACTION100
2.05-2.140.21571410.18092111X-RAY DIFFRACTION100
2.14-2.250.2361420.20082105X-RAY DIFFRACTION100
2.25-2.40.20241420.19422119X-RAY DIFFRACTION100
2.4-2.580.18781420.17592125X-RAY DIFFRACTION100
2.58-2.840.17971440.17842142X-RAY DIFFRACTION100
2.84-3.250.1951440.18362159X-RAY DIFFRACTION100
3.25-4.090.18971460.17442163X-RAY DIFFRACTION98
4.09-21.90.21381530.17472320X-RAY DIFFRACTION99

+
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