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- PDB-1dly: X-RAY CRYSTAL STRUCTURE OF HEMOGLOBIN FROM THE GREEN UNICELLULAR ... -

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Basic information

Entry
Database: PDB / ID: 1dly
TitleX-RAY CRYSTAL STRUCTURE OF HEMOGLOBIN FROM THE GREEN UNICELLULAR ALGA CHLAMYDOMONAS EUGAMETOS
ComponentsHEMOGLOBIN
KeywordsOXYGEN STORAGE/TRANSPORT / GLOBIN FOLD TRUNCATED HEMOGLOBIN / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


chloroplast / oxygen carrier activity / 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 / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Group 1 truncated hemoglobin LI637
Similarity search - Component
Biological speciesChlamydomonas eugametos (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsPesce, A. / Couture, M. / Guertin, M. / Dewilde, S. / Moens, L. / Bolognesi, M.
CitationJournal: EMBO J. / Year: 2000
Title: A novel two-over-two alpha-helical sandwich fold is characteristic of the truncated hemoglobin family.
Authors: Pesce, A. / Couture, M. / Dewilde, S. / Guertin, M. / Yamauchi, K. / Ascenzi, P. / Moens, L. / Bolognesi, M.
History
DepositionDec 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7926
Polymers17,8951
Non-polymers8975
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.598, 53.082, 67.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HEMOGLOBIN /


Mass: 17895.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas eugametos (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: Q08753

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Non-polymers , 5 types, 191 molecules

#2: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTruncated hemoglobin, with 121 amino acid residues per chain.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 28.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulphate, sodium acetate, cyanide, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 K / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
255 %ammonium sulfate1reservoir
350 mMsodium acetate1reservoir
45 mMpotassium cyanide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 2, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 11357 / % possible obs: 98 % / Redundancy: 3 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 2 % / Rmerge(I) obs: 0.126 / Num. unique all: 1252 / % possible all: 99.6
Reflection
*PLUS
Num. all: 12839 / % possible obs: 98.6 % / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 99.6 % / Mean I/σ(I) obs: 10

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Processing

Software
NameClassification
PHASESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1135 -random
Rwork0.192 ---
all0.192 11357 --
obs0.192 11357 10 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 59 186 1180
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.65
X-RAY DIFFRACTIONc_bond_d0.018
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.211 / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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