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- PDB-2ekt: Crystal structure of myoglobin reconstituted with 6-methyl-6-depr... -

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Basic information

Entry
Database: PDB / ID: 2ekt
TitleCrystal structure of myoglobin reconstituted with 6-methyl-6-depropionatehemin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / globin fold / OXYGEN STORAGE-TRANSPORT COMPLEX
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
6-METHY-6-DEPROPIONATEHEMIN / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsHarada, K. / Makino, M. / Sugimoto, H. / Hirota, S. / Matsuo, T. / Shiro, Y. / Hisaeda, Y. / Hayashi, T.
CitationJournal: Biochemistry / Year: 2007
Title: Structure and ligand binding properties of myoglobins reconstituted with monodepropionated heme: functional role of each heme propionate side chain
Authors: Harada, K. / Makino, M. / Sugimoto, H. / Hirota, S. / Matsuo, T. / Shiro, Y. / Hisaeda, Y. / Hayashi, T.
History
DepositionMar 25, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _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)18,1786
Polymers17,2351
Non-polymers9435
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.248, 90.248, 45.346
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-1260-

HOH

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Components

#1: Protein Myoglobin /


Mass: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / Tissue: Skeletal Muscle / References: UniProt: P02185
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-6HE / 6-METHY-6-DEPROPIONATEHEMIN


Mass: 558.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H30FeN4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 3.0M ammonium sulfate, 100mM bis-tris propane, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.78 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 18, 2004
RadiationMonochromator: SI(III) MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.78 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 85421 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 23.5 % / Rsym value: 0.062 / Net I/σ(I): 38.7
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 8466 / Rsym value: 0.349 / % possible all: 100

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JW8

1jw8


Resolution: 1.1→10 Å / Num. parameters: 14631 / Num. restraintsaints: 17821 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.158 4272 5.3 %RANDOM
all0.1327 81016 --
obs0.1311 81016 95 %-
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 1095 / Occupancy sum non hydrogen: 1577.33
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 59 303 1578
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0.049
X-RAY DIFFRACTIONs_from_restr_planes0.0235
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.094

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