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- PDB-4ns2: Crystal structure of Horse heart ferric myoglobin; D44K/D60K/E85K... -

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Basic information

Entry
Database: PDB / ID: 4ns2
TitleCrystal structure of Horse heart ferric myoglobin; D44K/D60K/E85K mutant
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / 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 speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsSpan, I. / Rosenzweig, A.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Charge-Disproportionation Symmetry Breaking Creates a Heterodimeric Myoglobin Complex with Enhanced Affinity and Rapid Intracomplex Electron Transfer.
Authors: Trana, E.N. / Nocek, J.M. / Woude, J.V. / Span, I. / Smith, S.M. / Rosenzweig, A.C. / Hoffman, B.M.
History
DepositionNov 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
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)17,8563
Polymers17,1431
Non-polymers7132
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.820, 30.360, 56.990
Angle α, β, γ (deg.)90.00, 97.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 17142.961 Da / Num. of mol.: 1 / Mutation: D44K, D60K, E85K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P68082
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.3 M ammonium sulfate, 0.1 M Tris pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.18→30.36 Å / Num. all: 48175 / Num. obs: 47934 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 9.18 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.18-1.213.70.70223476198.1
5.28-30.366.70.06342.2588199.4

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Processing

Software
NameVersionClassification
MD2data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YMB

1ymb


Resolution: 1.18→28.26 Å / SU ML: 0.11 / σ(F): 0 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 1954 4.19 %RANDOM
Rwork0.1698 ---
obs0.1709 46602 96.7 %-
all-48175 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.18→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 48 113 1362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061282
X-RAY DIFFRACTIONf_angle_d1.0871734
X-RAY DIFFRACTIONf_dihedral_angle_d14.977464
X-RAY DIFFRACTIONf_chiral_restr0.036178
X-RAY DIFFRACTIONf_plane_restr0.005213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.20950.28811290.25832931X-RAY DIFFRACTION90
1.2095-1.24220.2611310.2383018X-RAY DIFFRACTION92
1.2422-1.27880.2731350.21133000X-RAY DIFFRACTION92
1.2788-1.320.19821350.1963081X-RAY DIFFRACTION94
1.32-1.36720.23711380.18183122X-RAY DIFFRACTION96
1.3672-1.4220.18221390.16593185X-RAY DIFFRACTION97
1.422-1.48670.18111410.14933225X-RAY DIFFRACTION98
1.4867-1.56510.17921400.13713212X-RAY DIFFRACTION98
1.5651-1.66310.19721420.14173268X-RAY DIFFRACTION99
1.6631-1.79150.16521440.14593297X-RAY DIFFRACTION99
1.7915-1.97170.16221420.14993267X-RAY DIFFRACTION99
1.9717-2.25690.13891450.15313303X-RAY DIFFRACTION100
2.2569-2.84310.17681430.1723320X-RAY DIFFRACTION100
2.8431-28.26830.22251500.18013419X-RAY DIFFRACTION100

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