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- PDB-2spn: A NOVEL SITE-DIRECTED MUTANT OF MYOGLOBIN WITH AN UNUSUALLY HIGH ... -

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Basic information

Entry
Database: PDB / ID: 2spn
TitleA NOVEL SITE-DIRECTED MUTANT OF MYOGLOBIN WITH AN UNUSUALLY HIGH O2 AFFINITY AND LOW AUTOOXIDATION RATE
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Globin / Myoglobin / Globin-like superfamily / Globin/Protoglobin / Globin / Globin family profile.
Myoglobin
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsQuillin, M.L. / Arduini, R.M. / Phillips Jr., G.N.
Citation
Journal: J.Biol.Chem. / Year: 1992
Title: A novel site-directed mutant of myoglobin with an unusually high O2 affinity and low autooxidation rate.
Authors: Carver, T.E. / Brantley Jr., R.E. / Singleton, E.W. / Arduini, R.M. / Quillin, M.L. / Phillips Jr., G.N. / Olson, J.S.
#1: Journal: Proteins / Year: 1990
Title: Crystal Structure of Myoglobin from a Synthetic Gene
Authors: Phillips Jr., G.N. / Arduini, R.M. / Springer, B.A. / Sligar, S.G.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: High-Level Expression of Sperm Whale Myoglobin in Escherichia Coli
Authors: Springer, B.A. / Sligar, S.G.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 25, 1993-
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1444
Polymers17,3991
Non-polymers7453
Water2,234124
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)91.200, 91.200, 45.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Atom site foot note1: THIS OXYGEN IS COORDINATED TO FE IN THE HEM GROUP.

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Components

#1: Protein/peptide MYOGLOBIN /


Mass: 17399.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Heme
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-ID
120 mg/mlproteindrop
22.6-2.8 Mammonium sulfatedrop
320 mMTris-HClreservoir
41 mMEDTAreservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 18399 / % possible obs: 76 % / Num. measured all: 38051 / Rmerge(I) obs: 0.167

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.7→5 Å /
RfactorNum. reflection
Obs0.166 9172
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 50 124 1402
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
p_bond_d0.0190.02
p_angle_d0.0320.03
p_angle_deg
p_planar_d0.0570.06
p_hb_or_metal_coord
p_mcbond_it1.4431.5
p_mcangle_it1.9352
p_scbond_it2.973
p_scangle_it4.5514
p_plane_restr0.0260.03
p_chiral_restr0.1830.15
p_singtor_nbd0.2010.5
p_multtor_nbd0.3930.5
p_xhyhbond_nbd0.4610.5
p_xyhbond_nbd
p_planar_tor3.13
p_staggered_tor17.115
p_orthonormal_tor35.220
p_transverse_tor
p_special_tor

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