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- PDB-1m6c: V68N MYOGLOBIN WITH CO -

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Basic information

Entry
Database: PDB / ID: 1m6c
TitleV68N MYOGLOBIN WITH CO
ComponentsPROTEIN (MYOGLOBIN)
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN STORAGE / MYOGLOBIN / CO / OXYGEN STORAGE-TRANSPORT COMPLEX
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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.9 Å
AuthorsMurshudov, G.N. / Krzywda, S. / Brzozowski, A.M. / Jaskolski, M. / Scott, E.E. / Klizas, S.A. / Gibson, Q.H. / Olson, J.S. / Wilkinson, A.J.
CitationJournal: Biochemistry / Year: 1998
Title: Stabilizing bound O2 in myoglobin by valine68 (E11) to asparagine substitution.
Authors: Krzywda, S. / Murshudov, G.N. / Brzozowski, A.M. / Jaskolski, M. / Scott, E.E. / Klizas, S.A. / Gibson, Q.H. / Olson, J.S. / Wilkinson, A.J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 19, 1998Provider: 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MYOGLOBIN)
B: PROTEIN (MYOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2866
Polymers33,9972
Non-polymers1,2894
Water8,773487
1
A: PROTEIN (MYOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6433
Polymers16,9981
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (MYOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6433
Polymers16,9981
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)122.140, 42.300, 91.550
Angle α, β, γ (deg.)90.00, 92.49, 90.00
Int Tables number5
Space group name H-MI1211

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Components

#1: Protein/peptide PROTEIN (MYOGLOBIN)


Mass: 16998.416 Da / Num. of mol.: 2 / Mutation: V68N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Plasmid: PLCII / Production host: Escherichia coli (E. coli) / References: UniProt: P02189
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Heme
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO / Carbon monoxide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growpH: 7.1 / Details: 0.1 PHOSPHATE BUFFER PH 7.1 10 MG/ML PROTEIN
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS

Crystal-ID: 1 / Sol-ID: drop

IDConc.Common name
172-80 %(v/v)satammonium sulfate
20.1 Mphosphate
310 mg/mlprotein

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→24 Å / Num. obs: 35786 / % possible obs: 94 % / Redundancy: 4 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 22.3
Reflection
*PLUS
Highest resolution: 1.9 Å / % possible obs: 94.7 % / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Rmerge(I) obs: 0.214

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 1.9→24 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1788 5 %RANDOM
Rwork0.1921 ---
Obs-35786 94 %-
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å21.08 Å2
2--2.44 Å20 Å2
3----4.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 90 487 3049
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
p_bond_d0.0190.02
p_angle_d0.0370.04
p_angle_deg
p_planar_d0.0420.05
p_hb_or_metal_coord
p_mcbond_it3.3464
p_mcangle_it4.4196
p_scbond_it3.6964
p_scangle_it5.3036
p_plane_restr0.01420.02
p_chiral_restr0.1640.15
p_singtor_nbd0.1920.3
p_multtor_nbd0.2740.3
p_xhyhbond_nbd
p_xyhbond_nbd
p_planar_tor3.77
p_staggered_tor16.215
p_orthonormal_tor
p_transverse_tor42.420
p_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.192
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal target
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.15
X-RAY DIFFRACTIONp_mcbond_it4
X-RAY DIFFRACTIONp_scbond_it4
X-RAY DIFFRACTIONp_mcangle_it6
X-RAY DIFFRACTIONp_scangle_it6

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