[English] 日本語
Yorodumi
- PDB-6hbw: Crystal structure of deoxy-human hemoglobin beta6 glu->trp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hbw
TitleCrystal structure of deoxy-human hemoglobin beta6 glu->trp
Components
  • PROTEIN (HEMOGLOBIN ALPHA 1)
  • PROTEIN (HEMOGLOBIN BETA)
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT / HEMOGLOBIN / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / oxygen carrier activity / hydrogen peroxide catabolic process / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Heme signaling / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / platelet aggregation / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHarrington, D.J. / Adachi, K. / Royer Jr., W.E.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Crystal structure of deoxy-human hemoglobin beta6 Glu --> Trp. Implications for the structure and formation of the sickle cell fiber.
Authors: Harrington, D.J. / Adachi, K. / Royer Jr., W.E.
History
DepositionSep 10, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: 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: PROTEIN (HEMOGLOBIN ALPHA 1)
B: PROTEIN (HEMOGLOBIN BETA)
C: PROTEIN (HEMOGLOBIN ALPHA 1)
D: PROTEIN (HEMOGLOBIN BETA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6618
Polymers62,1954
Non-polymers2,4664
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.950, 81.280, 111.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PROTEIN (HEMOGLOBIN ALPHA 1) / HEMOGLOBIN A


Mass: 15150.353 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: RED BLOOD CELLS / Cellular location: CYTOPLASM / Plasmid: PGS389 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): GSY112 / References: UniProt: P69905
#2: Protein PROTEIN (HEMOGLOBIN BETA) / HEMOGLOBIN B


Mass: 15947.296 Da / Num. of mol.: 2 / Mutation: E6W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: RED BLOOD CELLS / Cellular location: CYTOPLASM / Plasmid: PGS389 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): GSY112 / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growpH: 7
Details: PROTEIN WAS RESUSPENDED IN 30 MM PHOSPHATE BUFFER, PH 7.0, DEOXYGENATED AND CONCENTRATED TO 160 MG/ML. PROTEIN WAS CRYSTALLIZED IN AN ANAEROBIC CHAMBER IN TUBE CONTAINING 10 UL PROTEIN ...Details: PROTEIN WAS RESUSPENDED IN 30 MM PHOSPHATE BUFFER, PH 7.0, DEOXYGENATED AND CONCENTRATED TO 160 MG/ML. PROTEIN WAS CRYSTALLIZED IN AN ANAEROBIC CHAMBER IN TUBE CONTAINING 10 UL PROTEIN SOLUTION, 5 UL CITRATE BUFFER (PH 4.0), AND 4UL OF 33% PEG 8K.
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
133 %PEG800011
2200 mMsodium citrate11
3160 mg/mlHbbeta6W11
430 mMphosphate11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 35597 / % possible obs: 89.2 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.076
Reflection shellResolution: 2→2.09 Å / Rsym value: 0.371 / % possible all: 70.3
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 112861 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 70.3 % / Rmerge(I) obs: 0.371

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HHB

2hhb


Resolution: 2→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3260377.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3354 10.2 %RANDOM
Rwork0.198 ---
obs0.198 33002 84.6 %-
Displacement parametersBiso mean: 14 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-8 Å
Luzzati sigma a0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4394 0 172 369 4935
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.68
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.541.5
X-RAY DIFFRACTIONx_mcangle_it2.252
X-RAY DIFFRACTIONx_scbond_it13.552
X-RAY DIFFRACTIONx_scangle_it8.842.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.27 346 10.2 %
Rwork0.228 3038 -
obs--70.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.PEP
X-RAY DIFFRACTION4PARAM19X.HEMETOPH19X.HEME
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 35002 / Num. reflection Rfree: 2112
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.829
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.586

+
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