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- PDB-5zzg: X-ray structure of F43Y/H64D sperm whale myoglobin in complex with TCP -

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Basic information

Entry
Database: PDB / ID: 5zzg
TitleX-ray structure of F43Y/H64D sperm whale myoglobin in complex with TCP
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / myoglobin
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / 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 / 2,4,6-trichlorophenol / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYuan, H. / Lin, Y.W.
CitationJournal: Acs Catalysis / Year: 2018
Title: A Rationally Designed Myoglobin Exhibits a Catalytic Dehalogenation Efficiency More than 1000-Fold That of a Native Dehaloperoxidase
Authors: Yin, L.L. / Yuan, H. / Liu, C. / He, B. / Gao, S.Q. / Wen, G.B. / Tan, X. / Lin, Y.W.
History
DepositionJun 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0423
Polymers17,2281
Non-polymers8142
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-19 kcal/mol
Surface area7890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.899, 49.477, 77.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myoglobin


Mass: 17227.893 Da / Num. of mol.: 1 / Mutation: F43Y/H64D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-T6C / 2,4,6-trichlorophenol


Mass: 197.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H3Cl3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG8000, 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 14844 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.047 / Rsym value: 0.088 / Net I/σ(I): 24.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 710 / Rpim(I) all: 0.294 / Rsym value: 0.78 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EB8

2eb8


Resolution: 1.8→35.46 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.04 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22897 749 5.1 %RANDOM
Rwork0.18457 ---
obs0.18679 14051 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.197 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20 Å2
2--0.04 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.8→35.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 53 107 1375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191358
X-RAY DIFFRACTIONr_bond_other_d0.0020.021314
X-RAY DIFFRACTIONr_angle_refined_deg3.1232.0051849
X-RAY DIFFRACTIONr_angle_other_deg0.9933034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6224.74659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.038154
X-RAY DIFFRACTIONr_chiral_restr0.1620.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021537
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02313
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7442.74638
X-RAY DIFFRACTIONr_mcbond_other2.7332.737635
X-RAY DIFFRACTIONr_mcangle_it3.9674.096804
X-RAY DIFFRACTIONr_mcangle_other3.9574.094803
X-RAY DIFFRACTIONr_scbond_it3.7323.312720
X-RAY DIFFRACTIONr_scbond_other3.7013.301717
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.644.7481042
X-RAY DIFFRACTIONr_long_range_B_refined8.94424.6491725
X-RAY DIFFRACTIONr_long_range_B_other8.90224.3931682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.796→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 55 -
Rwork0.212 977 -
obs--96 %

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