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- PDB-1uvx: Heme-ligand tunneling on group I truncated hemoglobins -

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Basic information

Entry
Database: PDB / ID: 1uvx
TitleHeme-ligand tunneling on group I truncated hemoglobins
ComponentsGLOBIN LI637
KeywordsOXYGEN STORAGE/TRANSPORT / LIGAND DIFFUSION / 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 / XENON / Group 1 truncated hemoglobin LI637
Similarity search - Component
Biological speciesCHLAMYDOMONAS MOEWUSII (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMilani, M. / Pesce, A. / Ouellet, Y. / Dewilde, S. / Friedman, J. / Ascenzi, P. / Guertin, M. / Bolognesi, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Heme-Ligand Tunneling in Group I Truncated Hemoglobins
Authors: Milani, M. / Pesce, A. / Ouellet, Y. / Dewilde, S. / Friedman, J. / Ascenzi, P. / Guertin, M. / Bolognesi, M.
History
DepositionJan 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLOBIN LI637
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4837
Polymers13,3151
Non-polymers1,1686
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)34.499, 52.932, 66.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLOBIN LI637 / HEMOGLOBIN


Mass: 13315.060 Da / Num. of mol.: 1 / Fragment: HEMOGLOBIN, RESIDUES 44-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS MOEWUSII (plant) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q08753
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Xe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRUNCATED HEMOGLOBIN, WITH 121 AMINO ACID RESIDUES PER CHAIN, WITH XE ATOMS DIFFUSED THROUGH THE ...TRUNCATED HEMOGLOBIN, WITH 121 AMINO ACID RESIDUES PER CHAIN, WITH XE ATOMS DIFFUSED THROUGH THE PROTEIN MATRIX

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.5
Details: AMMONIUM SULPHATE, SODIUM ACETATE, CYANIDE, pH 5.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5 / Method: vapor diffusion / Details: Pesce, A., (2000) EMBO J., 19, 2424.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
235 %ammonium sulfate1reservoir
350 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 4801 / % possible obs: 98.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 8
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.8 / % possible all: 95.4
Reflection
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 30 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.154
Reflection shell
*PLUS
% possible obs: 95.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLY

1dly


Resolution: 2.45→30 Å / SU B: 10.248 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.038 / ESU R Free: 0.33
RfactorNum. reflection% reflectionSelection details
Rfree0.268 483 10 %RANDOM
Rwork0.21 ---
obs0.216 4286 100 %-
Displacement parametersBiso mean: 30.576 Å2
Baniso -1Baniso -2Baniso -3
1-3.58 Å20 Å20 Å2
2---1.48 Å20 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 49 31 1015
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.003
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg0.572

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