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- PDB-1bin: LEGHEMOGLOBIN A (ACETOMET) -

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Basic information

Entry
Database: PDB / ID: 1bin
TitleLEGHEMOGLOBIN A (ACETOMET)
ComponentsLEGHEMOGLOBIN A
KeywordsOXYGEN TRANSPORT / HEME / NITROGEN FIXATION / MULTIGENE FAMILY
Function / homology
Function and homology information


nodulation / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Leghaemoglobin / Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Globin/Protoglobin / Globin family profile. / Globins / Globin / Globin / Globin-like / Globin-like superfamily ...Leghaemoglobin / Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Globin/Protoglobin / Globin family profile. / Globins / Globin / Globin / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Leghemoglobin A
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsBrucker, E.A. / Hargrove, M.S. / Phillips Jr., G.N.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Characterization of recombinant soybean leghemoglobin a and apolar distal histidine mutants.
Authors: Hargrove, M.S. / Barry, J.K. / Brucker, E.A. / Berry, M.B. / Phillips Jr., G.N. / Olson, J.S. / Arredondo-Peter, R. / Dean, J.M. / Klucas, R.V. / Sarath, G.
History
DepositionAug 23, 1996-
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEGHEMOGLOBIN A
B: LEGHEMOGLOBIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9687
Polymers30,5212
Non-polymers1,4475
Water2,432135
1
A: LEGHEMOGLOBIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0324
Polymers15,2601
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LEGHEMOGLOBIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9363
Polymers15,2601
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)34.980, 53.390, 141.730
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 LEGHEMOGLOBIN A


Mass: 15260.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ACETOMET / Source: (gene. exp.) Glycine max (soybean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02238
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.8 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMprotein1drop
20.1 Msodium phosphate1drop
32.4 Mammonium sulfate1reservoir
40.5 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 26287 / % possible obs: 85.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.103
Reflection
*PLUS
Highest resolution: 2.2 Å / % possible obs: 90 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.297 -10 %
Rwork0.198 --
obs0.198 12099 85.7 %
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 0 102 410 3138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg1.93
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.29
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.HEMETOPOLOGY.HEME
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.29

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