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- PDB-4of9: Structure of K42N variant of sperm whale myoglobin -

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Basic information

Entry
Database: PDB / ID: 4of9
TitleStructure of K42N variant of sperm whale myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / globin
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 domain 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.241 Å
AuthorsLebioda, L. / Wang, C. / Lovelace, L.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity.
Authors: Wang, C. / Lovelace, L.L. / Sun, S. / Dawson, J.H. / Lebioda, L.
History
DepositionJan 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4079
Polymers17,2201
Non-polymers1,1878
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.304, 90.304, 45.314
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

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Components

#1: Protein Myoglobin


Mass: 17219.875 Da / Num. of mol.: 1 / Mutation: K42N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 2.7 M ammonium sulfate, 20 mM Tris, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.241→24.76 Å / Num. obs: 58965 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 36.1
Reflection shellResolution: 1.241→1.273 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.209 / Num. unique all: 3753 / % possible all: 90.4

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OCK

3ock
PDB Unreleased entry


Resolution: 1.241→24.76 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.69 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14123 2983 5.1 %RANDOM
Rwork0.11854 ---
obs0.11969 55979 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.499 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å20 Å2
2--0.08 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.241→24.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 75 311 1602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0191373
X-RAY DIFFRACTIONr_bond_other_d0.0030.021352
X-RAY DIFFRACTIONr_angle_refined_deg2.772.0181865
X-RAY DIFFRACTIONr_angle_other_deg1.15233129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1925168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6624.56157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11615257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.437154
X-RAY DIFFRACTIONr_chiral_restr0.190.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021509
X-RAY DIFFRACTIONr_gen_planes_other0.010.02311
X-RAY DIFFRACTIONr_mcbond_it1.3470.73629
X-RAY DIFFRACTIONr_mcbond_other1.3470.728628
X-RAY DIFFRACTIONr_mcangle_it1.8141.101789
X-RAY DIFFRACTIONr_mcangle_other1.8141.103790
X-RAY DIFFRACTIONr_scbond_it2.271.012744
X-RAY DIFFRACTIONr_scbond_other2.2551.012744
X-RAY DIFFRACTIONr_scangle_other2.3341.4171070
X-RAY DIFFRACTIONr_long_range_B_refined4.7069.5071986
X-RAY DIFFRACTIONr_long_range_B_other3.2027.2441745
X-RAY DIFFRACTIONr_rigid_bond_restr8.35332724
X-RAY DIFFRACTIONr_sphericity_free52.813548
X-RAY DIFFRACTIONr_sphericity_bonded9.9352952
LS refinement shellResolution: 1.241→1.273 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 208 -
Rwork0.159 3753 -
obs--90.39 %

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