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- PDB-1ufp: Crystal Structure of an Artificial Metalloprotein:Fe(III)(3,3'-Me... -

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Basic information

Entry
Database: PDB / ID: 1ufp
TitleCrystal Structure of an Artificial Metalloprotein:Fe(III)(3,3'-Me2-salophen)/apo-wild type Myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / myoglobin / Schiff base / iron / salophen / metalloprotein / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globins / Globin / Globin / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsUeno, T. / Ohashi, M. / Kono, M. / Kondo, K. / Suzuki, A. / Yamane, T. / Watanabe, Y.
CitationJournal: Inorg.Chem. / Year: 2004
Title: Crystal Structures of Artificial Metalloproteins: Tight Binding of Fe(III)(Schiff-Base) by Mutation of Ala71 to Gly in Apo-Myoglobin
Authors: Ueno, T. / Ohashi, M. / Kono, M. / Kondo, K. / Suzuki, A. / Yamane, T. / Watanabe, Y.
History
DepositionJun 4, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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)17,9367
Polymers17,3661
Non-polymers5706
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.054, 58.817, 75.619
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 Myoglobin /


Mass: 17366.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: puc19 / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: sodium, potassium phosphate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 3, 2002
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 8790 / Num. obs: 7824 / % possible obs: 96.1 % / Observed criterion σ(I): 0.5 / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 4.4 / % possible all: 94

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1UFJ
Resolution: 2.1→30.29 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 225555.4 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 439 5.6 %RANDOM
Rwork0.207 ---
obs-7824 86.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 86.2923 Å2 / ksol: 0.387836 e/Å3
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2--2.64 Å20 Å2
3----3.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 30 156 1411
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 58 5.5 %
Rwork0.208 990 -
obs--70.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION5CZM.PARAMCZM.TOP

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