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- PDB-2blj: Structure of L29W MbCO -

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Basic information

Entry
Database: PDB / ID: 2blj
TitleStructure of L29W MbCO
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / MYOGLOBIN / MUTANT / HEME
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPHYSETER CATODON (sperm whale)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.8 Å
AuthorsNienhaus, K. / Ostermann, A. / Nienhaus, G.U. / Parak, F.G. / Schmidt, M.
CitationJournal: Biochemistry / Year: 2005
Title: Ligand Migration and Protein Fluctuations in Myoglobin Mutant L29W
Authors: Nienhaus, K. / Ostermann, A. / Nienhaus, G.U. / Parak, F.G. / Schmidt, M.
History
DepositionMar 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 27, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9523
Polymers17,3071
Non-polymers6442
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.870, 91.870, 46.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein MYOGLOBIN


Mass: 17307.020 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYSETER CATODON (sperm whale) / Tissue: MUSCLE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02185
#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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
Sequence detailsSEQUENCE REVISION TO CHAIN A 122, ASP TO ASN. REFERENCE: ROMERO-HERRERA A.E., LEHMANN H. RESIDUE ...SEQUENCE REVISION TO CHAIN A 122, ASP TO ASN. REFERENCE: ROMERO-HERRERA A.E., LEHMANN H. RESIDUE 122 OF SPERM WHALE AND HORSE MYOGLOBIN. BIOCHIM. BIOPHYS. ACTA 336:318-323(1974).

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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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growpH: 7.8 / Details: pH 7.80

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: BRUKER MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 12, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 73405 / % possible obs: 80 % / Redundancy: 4.5 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / % possible all: 61

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Processing

Software
NameVersionClassification
CNS1.1refinement
SAINTdata reduction
SAINTdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.8→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 827 4 %RANDOM
Rwork0.2238 ---
obs0.2238 16299 78.6 %-
Solvent computationBsol: 50.1287 Å2 / ksol: 0.359627 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.406 Å2-4.183 Å20 Å2
2--0.406 Å20 Å2
3----0.811 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 45 0 1268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006543
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.0146
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19XAO.HEME
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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