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- PDB-2blh: Ligand Migration and Protein Fluctuations in Myoglobin Mutant L29W -

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Basic information

Entry
Database: PDB / ID: 2blh
TitleLigand Migration and Protein Fluctuations in Myoglobin Mutant L29W
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / MYOGLOBIN / MUTANT / HEME
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPHYSETER CATODON (sperm whale)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.77 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 1.1Dec 10, 2014Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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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)17,9242
Polymers17,3071
Non-polymers6161
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.420, 92.420, 46.790
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
Details: SLOW CO REBINDER / Source: (gene. exp.) PHYSETER CATODON (sperm whale) / Tissue: MUSCLESkeletal muscle / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 29 TO TRP
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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growpH: 7.8
Details: 2.8 M AMMONIUM SULFATE, 25 MM TRIS, 1 MM EDTA, PH 8.0

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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 19, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 81268 / % possible obs: 89.4 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.1
Reflection shellResolution: 1.77→1.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.2 / % possible all: 51

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Processing

Software
NameVersionClassification
CNS1.1refinement
SAINTdata reduction
SAINTdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.77→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHODD
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 1905 8.8 %RANDOM
Rwork0.1865 ---
obs0.1865 19438 89.6 %-
Solvent computationBsol: 62.5483 Å2 / ksol: 0.34319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.553 Å2-1.271 Å20 Å2
2--0.553 Å20 Å2
3----1.106 Å2
Refinement stepCycle: LAST / Resolution: 1.77→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 43 131 1397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007503
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_deg1.03067
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 file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3PARAM19X.HEME

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