[English] 日本語
Yorodumi
- PDB-6zmx: Crystal structure of hemoglobin from turkey (Meleagiris gallopova... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zmx
TitleCrystal structure of hemoglobin from turkey (Meleagiris gallopova) crystallized in orthorhombic form at 1.4 Angstrom resolution
Components
  • Hemoglobin beta chain
  • Hemoglobin subunit alpha-A
KeywordsOXYGEN STORAGE/OXYGEN TRANSPORT / Hemoglobin / turkey / heme / meleagiris gallopova / orthorhombic form / OXYGEN TRANSPORT / OXYGEN STORAGE / OXYGEN STORAGE-OXYGEN TRANSPORT complex
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-A / Hemoglobin beta chain
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.389 Å
AuthorsPandian, R. / Shobana, N. / Sundaresan, S.S. / Sayed, Y. / Ponnuswamy, M.N.
Funding support United Kingdom, Portugal, 2items
OrganizationGrant numberCountry
Science and Technology Funding CouncilST/R002754/1 United Kingdom
Foundation for Science and Technology (FCT)UIDB/04378/2020 Portugal
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural studies of hemoglobin from two flightless birds, ostrich and turkey: insights into their differing oxygen-binding properties.
Authors: Ramesh, P. / Sundaresan, S.S. / Shobana, N. / Vinuchakkaravarthy, T. / Sivakumar, K. / Yasien, S. / Ponnuswamy, M.N.G.
History
DepositionJul 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Derived calculations / Structure summary / Category: struct_conn / struct_keywords
Item: _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id ..._struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 31, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,8189
Polymers63,3294
Non-polymers2,4895
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-101 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.760, 82.140, 90.540
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
11(chain A and (resseq 1:40 or resseq 42:67 or resseq...
21(chain C and (resseq 1:40 or resseq 42:67 or resseq...
12(chain D and (resseq 1:13 or (resid 14 and (name...
22(chain B and (resseq 1:13 or (resid 14 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 40
121(chain A and (resseq 1:40 or resseq 42:67 or resseq...A42 - 67
131(chain A and (resseq 1:40 or resseq 42:67 or resseq...A69 - 81
141(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
151(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
161(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
171(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
181(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
191(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
1101(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
1111(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
211(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 40
221(chain C and (resseq 1:40 or resseq 42:67 or resseq...C42 - 67
231(chain C and (resseq 1:40 or resseq 42:67 or resseq...C0
241(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
251(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
261(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
271(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
281(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
291(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
2101(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
112(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 13
122(chain D and (resseq 1:13 or (resid 14 and (name...D14
132(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 150
142(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 150
152(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 150
162(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 150
172(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 150
212(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 13
222(chain B and (resseq 1:13 or (resid 14 and (name...B14
232(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 150
242(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 150
252(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 150
262(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 150
272(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 150

NCS ensembles :
ID
1
2

-
Components

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


Mass: 15334.737 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P81023
#2: Protein Hemoglobin beta chain


Mass: 16329.866 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P84479
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.25 Å3/Da / Density % sol: 45.46 % / Description: Block
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 40% of PEG 3350 in 50mM phosphate buffer at pH7.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.389→60.835 Å / Num. obs: 118908 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 26.287 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.096 / Net I/σ(I): 7.4
Reflection shellResolution: 1.389→1.413 Å / Redundancy: 4.4 % / Num. unique obs: 5867 / CC1/2: 0.514 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAW

1faw


Resolution: 1.389→60.835 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 5918 4.98 %
Rwork0.1969 112980 -
obs0.1983 118898 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.53 Å2 / Biso mean: 28.6232 Å2 / Biso min: 9.26 Å2
Refinement stepCycle: final / Resolution: 1.389→60.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 173 489 5064
Biso mean--24.28 41.15 -
Num. residues----568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074920
X-RAY DIFFRACTIONf_angle_d0.9056763
X-RAY DIFFRACTIONf_chiral_restr0.068740
X-RAY DIFFRACTIONf_plane_restr0.006842
X-RAY DIFFRACTIONf_dihedral_angle_d20.4021707
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1194X-RAY DIFFRACTION6.954TORSIONAL
12C1194X-RAY DIFFRACTION6.954TORSIONAL
21D1272X-RAY DIFFRACTION6.954TORSIONAL
22B1272X-RAY DIFFRACTION6.954TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3891-1.40490.42221890.3937370298
1.4049-1.42140.39671870.3822374299
1.4214-1.43880.38411730.3705373499
1.4388-1.4570.34811870.3528375299
1.457-1.47620.33751750.3518372599
1.4762-1.49640.3661920.3386374399
1.4964-1.51780.32131840.3312372599
1.5178-1.54040.30671820.3046375599
1.5404-1.56450.30692010.2805366197
1.5645-1.59020.29782140.2743375899
1.5902-1.61760.28812040.2501371399
1.6176-1.6470.25362290.23223735100
1.647-1.67870.24392190.22773751100
1.6787-1.71290.25291850.21183778100
1.7129-1.75020.23891830.21733783100
1.7502-1.79090.2431990.21263765100
1.7909-1.83570.23082170.20983751100
1.8357-1.88530.22441970.20823794100
1.8853-1.94080.22941830.19963803100
1.9408-2.00350.23191650.20193820100
2.0035-2.07510.23722080.20273777100
2.0751-2.15820.23081920.1904374798
2.1582-2.25640.22541960.187374098
2.2564-2.37530.20961940.1874377499
2.3753-2.52420.22211870.1844380599
2.5242-2.71910.22051820.1839382499
2.7191-2.99270.22552160.1867377798
2.9927-3.42570.22082330.177375698
3.4257-4.31590.1792230.1534378697
4.3159-60.8350.17782220.1634400498

+
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