[English] 日本語
Yorodumi
- PDB-6ii1: Crystal Structure Analysis of CO form hemoglobin from Bos taurus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ii1
TitleCrystal Structure Analysis of CO form hemoglobin from Bos taurus
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / heme binding / iron ion binding / Red blood cells / globin family
Function / homology
Function and homology information


Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding ...Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.34 Å
AuthorsKihira, K. / Morita, Y. / Yamada, T. / Kureishi, M. / Komatsu, T.
CitationJournal: J Phys Chem B / Year: 2018
Title: Quaternary Structure Analysis of a Hemoglobin Core in Hemoglobin-Albumin Cluster.
Authors: Morita, Y. / Yamada, T. / Kureishi, M. / Kihira, K. / Komatsu, T.
History
DepositionOct 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,78812
Polymers61,2104
Non-polymers2,5788
Water13,025723
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-107 kcal/mol
Surface area23900 Å2
Unit cell
Length a, b, c (Å)63.560, 76.283, 109.789
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA2 - 1372 - 137
21THRTHRCC2 - 1372 - 137
12ARGARGBB3 - 1442 - 143
22ARGARGDD3 - 1442 - 143

NCS ensembles :
ID
1
2

-
Components

#1: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 14627.623 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01966
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15977.382 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02070
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 6.8
Details: 25% PEG3,350 0.2 M MgCl2 0.2 M KCl 0.2 M NaCl 0.1 M HEPES pH6.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→48.83 Å / Num. obs: 120044 / % possible obs: 99.8 % / Redundancy: 14.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.021 / Rrim(I) all: 0.079 / Net I/σ(I): 20.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.34-1.3614.41.51758620.6940.4091.57299.6
7.34-48.83100.0467270.9960.0150.04985.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å48.83 Å
Translation2.5 Å48.83 Å

-
Processing

Software
NameVersionClassification
XDSJun 1, 2017data reduction
Aimless0.5.31data scaling
PHASER2.8.1phasing
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IHX

6ihx


Resolution: 1.34→48.83 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.027 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 1998 1.7 %RANDOM
Rwork0.1374 ---
obs0.138 117962 99.8 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 75.95 Å2 / Biso mean: 20.994 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--1.24 Å20 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 1.34→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 180 723 5197
Biso mean--17.55 35.98 -
Num. residues----563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0144637
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174253
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.7046345
X-RAY DIFFRACTIONr_angle_other_deg1.1641.6799859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0923.333192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43815721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5411512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025240
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02944
X-RAY DIFFRACTIONr_rigid_bond_restr2.31238890
X-RAY DIFFRACTIONr_sphericity_free34.5015176
X-RAY DIFFRACTIONr_sphericity_bonded14.90859307
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A42860.07
12C42860.07
21B45240.08
22D45240.08
LS refinement shellResolution: 1.34→1.375 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 145 -
Rwork0.23 8592 -
all-8737 -
obs--99.7 %

+
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