[English] 日本語
Yorodumi
- PDB-3a59: Structure of Hemoglobin from flightless bird (Struthio camelus) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3a59
TitleStructure of Hemoglobin from flightless bird (Struthio camelus)
Components
  • Hemoglobin subunit alpha-A
  • Hemoglobin subunit beta
KeywordsOXYGEN STORAGE / OXYGEN TRANSPORT / Ostrich / Struthio camelus / Hemoglobin / Heme / Iron / Metal-binding / Polymorphism / Transport
Function / homology
Function and homology information


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 ...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
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-A / Hemoglobin subunit beta
Similarity search - Component
Biological speciesStruthio camelus (African ostrich)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.41 Å
AuthorsJaimohan, S.M. / Naresh, M.D. / Mandal, A.B.
CitationJournal: to be published
Title: Structure of Hemoglobin from flightless bird (Struthio camelus)
Authors: Jaimohan, S.M. / Naresh, M.D. / Mandal, A.B.
History
DepositionAug 3, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemoglobin subunit alpha-A
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha-A
D: Hemoglobin subunit beta
E: Hemoglobin subunit alpha-A
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha-A
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,08716
Polymers127,1558
Non-polymers4,9328
Water00
1
A: Hemoglobin subunit alpha-A
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0224
Polymers31,7892
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-50 kcal/mol
Surface area13620 Å2
MethodPISA
2
C: Hemoglobin subunit alpha-A
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0224
Polymers31,7892
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-47 kcal/mol
Surface area13440 Å2
MethodPISA
3
E: Hemoglobin subunit alpha-A
F: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0224
Polymers31,7892
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-49 kcal/mol
Surface area13590 Å2
MethodPISA
4
G: Hemoglobin subunit alpha-A
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0224
Polymers31,7892
Non-polymers1,2332
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-48 kcal/mol
Surface area13510 Å2
MethodPISA
5
A: Hemoglobin subunit alpha-A
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha-A
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0438
Polymers63,5774
Non-polymers2,4664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-107 kcal/mol
Surface area24270 Å2
MethodPISA
6
E: Hemoglobin subunit alpha-A
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha-A
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0438
Polymers63,5774
Non-polymers2,4664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-108 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.051, 82.051, 214.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

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


Mass: 15470.804 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Struthio camelus (African ostrich) / References: UniProt: P01981
#2: Protein
Hemoglobin subunit beta / Hemoglobin beta chain / Beta-globin


Mass: 16317.874 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Struthio camelus (African ostrich) / References: UniProt: P02123
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 60% Poly ethylene glycol 3350, 50mM Sodium phosphate buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 18, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.41→28.75 Å / Num. obs: 13030 / Num. measured all: 43272
Reflection shellResolution: 3.41→3.54 Å / Rmerge(I) obs: 0.1509 / Mean I/σ(I) obs: 3.8 / Num. unique all: 13030

-
Processing

Software
NameVersionClassification
MAR345345data collection
PHASERphasing
REFMAC5.5.0066refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FS4

3fs4


Resolution: 3.41→28.75 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.741 / SU B: 56.434 / SU ML: 0.894 / Cross valid method: THROUGHOUT / ESU R Free: 1.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS: There are several close contacts as mentioned in remark 500 due to the low resolution(only 3.41A structure).
RfactorNum. reflection% reflectionSelection details
Rfree0.35371 1534 10.5 %RANDOM
Rwork0.26539 ---
obs0.2748 13030 75.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.031 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 3.41→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8970 0 344 0 9314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229582
X-RAY DIFFRACTIONr_angle_refined_deg0.942.05413108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.51251140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88523.918388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.083151552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6171536
X-RAY DIFFRACTIONr_chiral_restr0.0570.21428
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217184
X-RAY DIFFRACTIONr_mcbond_it0.3171.55714
X-RAY DIFFRACTIONr_mcangle_it0.5829184
X-RAY DIFFRACTIONr_scbond_it0.38933868
X-RAY DIFFRACTIONr_scangle_it0.6894.53924
LS refinement shellResolution: 3.414→3.501 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 83 -
Rwork0.351 812 -
obs--65.81 %

+
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