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- PDB-3sdn: Structure of G65I sperm whale myoglobin mutant -

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Basic information

Entry
Database: PDB / ID: 3sdn
TitleStructure of G65I sperm whale myoglobin mutant
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / globin fold / oxygen carrier / oxygen
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / 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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLebioda, L. / Huang, X.
CitationJournal: Biochemistry / Year: 2011
Title: Amphitrite ornata Dehaloperoxidase (DHP): Investigations of Structural Factors That Influence the Mechanism of Halophenol Dehalogenation Using "Peroxidase-like" Myoglobin Mutants and "Myoglobin-like" DHP Mutants.
Authors: Du, J. / Huang, X. / Sun, S. / Wang, C. / Lebioda, L. / Dawson, J.H.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,2225
Polymers17,4221
Non-polymers8004
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.036, 48.011, 77.557
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: 17422.252 Da / Num. of mol.: 1 / Mutation: G65I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 6.5
Details: 34% PEG 8000, 0.3 M sodium acetate, 0.1 M PIPES, pH 6.5, VAPOR DIFFUSION, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→44 Å / Num. obs: 24768 / % possible obs: 87.3 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.074

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OCK

3ock
PDB Unreleased entry


Resolution: 1.5→40.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.913 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23823 1102 5.1 %RANDOM
Rwork0.17695 ---
obs0.18011 20386 86.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.632 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2--0.78 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 55 80 1310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211257
X-RAY DIFFRACTIONr_angle_refined_deg2.032.0591705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1845151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14823.61747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16715211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.594154
X-RAY DIFFRACTIONr_chiral_restr0.1310.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021920
X-RAY DIFFRACTIONr_mcbond_it2.4251.5755
X-RAY DIFFRACTIONr_mcangle_it3.53321194
X-RAY DIFFRACTIONr_scbond_it5.5493502
X-RAY DIFFRACTIONr_scangle_it7.7114.5511
X-RAY DIFFRACTIONr_rigid_bond_restr2.97831257
LS refinement shellResolution: 1.496→1.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 40 -
Rwork0.146 748 -
obs--43.7 %

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