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- PDB-5zze: Crystal structure of horse myoglobin crystallized by ammonium sulfate -

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Basic information

Entry
Database: PDB / ID: 5zze
TitleCrystal structure of horse myoglobin crystallized by ammonium sulfate
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / DOMESTIC HORSE / EQUINE
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 / oxygen transport / 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
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.423 Å
AuthorsKitahara, M. / Fudo, S. / Yoneda, T. / Nukaga, M. / Hoshino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K08458 Japan
CitationJournal: Cryst.Growth Des. / Year: 2019
Title: Anisotropic Distribution of Ammonium Sulfate Ions in Protein Crystallization
Authors: Kitahara, M. / Fudo, S. / Yoneda, T. / Nukaga, M. / Hoshino, T.
History
DepositionJun 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 27, 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
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8315
Polymers16,9261
Non-polymers9054
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-20 kcal/mol
Surface area7740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.264, 28.588, 62.822
Angle α, β, γ (deg.)90.000, 105.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin /


Mass: 16926.463 Da / Num. of mol.: 1 / Fragment: UNP residues 2-153 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P68082
#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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.8 Å3/Da / Density % sol: 31.69 % / Mosaicity: 0.21 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 17, 2016 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→33.76 Å / Num. obs: 31280 / % possible obs: 98 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.36 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.085 / Rrim(I) all: 0.155 / Net I/σ(I): 4.5 / Num. measured all: 100278 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.27-1.292.52.50712820.1051.8143.11480.3
6.97-33.762.60.0622020.9880.0450.07791.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.343
Highest resolutionLowest resolution
Rotation33.77 Å1.76 Å

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Processing

Software
NameVersionClassificationNB
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimless0.1.27data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.423→33.759 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 26.24
RfactorNum. reflection% reflection
Rfree0.2477 1120 5 %
Rwork0.2024 --
obs0.2047 22397 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 45.83 Å2 / Biso mean: 20.862 Å2 / Biso min: 10.6 Å2
Refinement stepCycle: final / Resolution: 1.423→33.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 58 147 1400
Biso mean--20.16 28.36 -
Num. residues----152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4235-1.48820.35361300.30652484261493
1.4882-1.56670.29291420.266427002842100
1.5667-1.66490.31981420.247926942836100
1.6649-1.79340.30481420.22526972839100
1.7934-1.97390.27141440.20312726287099
1.9739-2.25940.24051400.18192664280499
2.2594-2.84640.24861400.19842668280897
2.8464-33.77520.21081400.18542644278494

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