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- PDB-4twu: Horse heart myoglobin mutant (D44K/D60K/E85K) with Zn-deuteroporp... -

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Basic information

Entry
Database: PDB / ID: 4twu
TitleHorse heart myoglobin mutant (D44K/D60K/E85K) with Zn-deuteroporphyrin IX
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Myoglobin / Zn-deuteroporphyrin IX
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
Zinc (II) Deuteroporphyrin IX / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.08 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
DepositionJul 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Aug 26, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.3Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)18,1016
Polymers17,1431
Non-polymers9585
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.660, 30.350, 56.940
Angle α, β, γ (deg.)90.000, 98.420, 90.000
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-ZND / Zinc (II) Deuteroporphyrin IX


Mass: 573.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28N4O4Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 120 / 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: 42.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris/HCl, 3.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.08→21.9 Å / Num. obs: 59805 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 12.916 Å2 / Rmerge F obs: 0.994 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.101 / Χ2: 0.968 / Net I/σ(I): 9.98 / Num. measured all: 297036
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.08-1.110.7020.5722.2212710453733700.66874.3
1.11-1.140.8490.4323.1917849449440980.49291.2
1.14-1.170.9320.334.4521156433241610.36796.1
1.17-1.210.940.295.0920830419240810.32297.4
1.21-1.250.9510.2535.7720491410940210.28297.9
1.25-1.290.9650.2126.7419728393838500.23697.8
1.29-1.340.9720.1837.6919126381437350.20397.9
1.34-1.390.9770.1628.5818512366736010.1898.2
1.39-1.460.980.149.718015355135040.15698.7
1.46-1.530.9860.11411.517066335733220.12799
1.53-1.610.9860.10512.7116469322132000.11799.3
1.61-1.710.9890.09713.8315596305630360.10899.3
1.71-1.830.9880.09414.7414547284228310.10599.6
1.83-1.970.9880.08516.2613630268426770.09599.7
1.97-2.160.9890.08117.4812469247024640.0999.8
2.16-2.410.990.07618.1211270222322190.08599.8
2.41-2.790.9910.07618.5410063199619930.08599.8
2.79-3.420.9910.07418.938386168916780.08399.3
3.42-4.830.9870.07418.676100132412810.08496.8
4.830.9840.07217.9130237616830.08389.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.08 Å21.9 Å
Translation1.08 Å21.9 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALE2.5.6data scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NS2

4ns2


Resolution: 1.08→21.9 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.034 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 2948 4.9 %RANDOM
Rwork0.1629 56849 --
obs0.164 59797 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.51 Å2 / Biso mean: 14.916 Å2 / Biso min: 5.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0.12 Å2
2--0.63 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.08→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 98 120 1419
Biso mean--20.91 23 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191354
X-RAY DIFFRACTIONr_bond_other_d0.0010.021311
X-RAY DIFFRACTIONr_angle_refined_deg1.2412.0011839
X-RAY DIFFRACTIONr_angle_other_deg0.75933032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3845158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.5112552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11715242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.545152
X-RAY DIFFRACTIONr_chiral_restr0.0840.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
X-RAY DIFFRACTIONr_mcbond_it1.6271.165620
X-RAY DIFFRACTIONr_mcbond_other1.6291.165621
X-RAY DIFFRACTIONr_mcangle_it2.2481.758776
X-RAY DIFFRACTIONr_rigid_bond_restr2.06432665
X-RAY DIFFRACTIONr_sphericity_free19.588528
X-RAY DIFFRACTIONr_sphericity_bonded10.43552721
LS refinement shellResolution: 1.08→1.108 Å
Num. reflection% reflection
Rfree162 -
Rwork3205 -
obs-74.24 %

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