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- PDB-4twv: Horse heart myoglobin mutant (K45E/K63E/K96E) with Zn-deuteroporp... -

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Basic information

Entry
Database: PDB / ID: 4twv
TitleHorse heart myoglobin mutant (K45E/K63E/K96E) with Zn-deuteroporphyrin IX
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Myoglobin / Zn-deuteroporphyrin IX
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
Zinc (II) Deuteroporphyrin IX / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.06 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)17,6882
Polymers17,1151
Non-polymers5741
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.530, 34.970, 123.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myoglobin /


Mass: 17114.512 Da / Num. of mol.: 1 / Mutation: K45E, K63E, K96E
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.81 Å3/Da / Density % sol: 32.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris/HCl, 2.8 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
ReflectionRedundancy: 6.6 % / Number: 367507 / Rmerge(I) obs: 0.064 / D res high: 1.06 Å / D res low: 28.53 Å / Num. obs: 55463 / % possible obs: 97
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
1.061.0910.5334.2
4.7428.5310.0285.8
ReflectionResolution: 1.06→28.53 Å / Num. obs: 55463 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 10.221 Å2 / Rmerge F obs: 0.999 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Rrim(I) all: 0.07 / Χ2: 1.019 / Net I/σ(I): 16.98 / Num. measured all: 367507
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allNum. measured allNum. unique allCC1/2Rpim(I) all
1.06-1.090.8010.5362.3812459413829860.61472.2
1.09-1.120.8890.4583.0716961405335430.51487.4
1.12-1.150.9350.3814.4424105395538790.41698.1
1.15-1.190.9650.3075.9226572386638660.332100
1.19-1.220.9730.2646.7925623371337120.285100
1.22-1.270.9780.2178.2825036360836080.235100
1.27-1.310.9850.1819.8124405350034980.19599.9
1.31-1.370.9880.15711.1623735337933790.17100
1.37-1.430.990.13513.0922777323432330.145100
1.43-1.50.9930.10616.5121964309530950.115100
1.5-1.580.9950.08719.5520942295229520.094100
1.58-1.680.9960.07622.5620096282528240.082100
1.68-1.790.9970.06725.7418561261526130.07399.9
1.79-1.940.9980.05630.0917556247324680.06199.8
1.94-2.120.9980.04735.1915949227122640.05199.7
2.12-2.370.9990.04139.2814676211421110.04499.9
2.37-2.740.9990.03641.5712638183618290.03999.6
2.74-3.350.9990.03244.5410749158715820.03599.7
3.35-4.745.80.9990.02946.288319127212680.03199.743847530.9990.012
1.09-4.744.20.9990.02842.9443847707530.0397.81245929860.7970.29

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.06 Å27.8 Å
Translation1.06 Å27.8 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: 3RJ6

3rj6


Resolution: 1.06→28.53 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.873 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1654 2690 4.9 %RANDOM
Rwork0.1479 52707 --
obs0.1488 55397 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.48 Å2 / Biso mean: 8.686 Å2 / Biso min: 3.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0 Å2
2---0.1 Å20 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 1.06→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 78 144 1421
Biso mean--6.35 16.22 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191321
X-RAY DIFFRACTIONr_bond_other_d0.0020.021249
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.9831795
X-RAY DIFFRACTIONr_angle_other_deg0.78432888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5195154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23825.43957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08915225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.458152
X-RAY DIFFRACTIONr_chiral_restr0.090.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02282
X-RAY DIFFRACTIONr_mcbond_it0.950.666613
X-RAY DIFFRACTIONr_mcbond_other0.9490.666614
X-RAY DIFFRACTIONr_mcangle_it1.391.003765
X-RAY DIFFRACTIONr_rigid_bond_restr2.65632570
X-RAY DIFFRACTIONr_sphericity_free19.252525
X-RAY DIFFRACTIONr_sphericity_bonded6.35252651
LS refinement shellResolution: 1.06→1.088 Å
Num. reflection% reflection
Rfree130 -
Rwork2854 -
obs-72.2 %

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