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- PDB-4fwx: Aquoferric F33Y CuB myoglobin (F33Y L29H F43H sperm whale myoglobin) -

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Basic information

Entry
Database: PDB / ID: 4fwx
TitleAquoferric F33Y CuB myoglobin (F33Y L29H F43H sperm whale myoglobin)
ComponentsMyoglobin
KeywordsTRANSPORT PROTEIN / Globin / Oxidase
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGao, Y.-G. / Stoner-Ma, D. / Robinson, H. / Petrik, I.D. / Miner, K.D. / Lu, Y.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: A Designed Functional Metalloenzyme that Reduces O(2) to H(2) O with Over One Thousand Turnovers.
Authors: Miner, K.D. / Mukherjee, A. / Gao, Y.G. / Null, E.L. / Petrik, I.D. / Zhao, X. / Yeung, N. / Robinson, H. / Lu, Y.
History
DepositionJul 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)17,8832
Polymers17,2671
Non-polymers6161
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.219, 47.718, 77.089
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: 17266.914 Da / Num. of mol.: 1 / Mutation: L29H, F33Y, F43H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3*) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: F33Y-CuBMb (1.0 mM) in 100 mM tris pH 8, (pH adjusted H2SO4), was mixed 1:3 with well buffer (0.1 M sodium cacodylate pH 6.5, 0.2 M sodium acetate trihydrate with 30% w/v polyethylene glycol ...Details: F33Y-CuBMb (1.0 mM) in 100 mM tris pH 8, (pH adjusted H2SO4), was mixed 1:3 with well buffer (0.1 M sodium cacodylate pH 6.5, 0.2 M sodium acetate trihydrate with 30% w/v polyethylene glycol 8000) using the hanging drop method with 300 uL well buffer in the well of the crystallization tray, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 12106 / Num. obs: 12106 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.118 / Net I/σ(I): 35.9
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameClassification
CBASSdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FWZ

4fwz


Resolution: 1.9→40.57 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.65 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26642 560 4.7 %RANDOM
Rwork0.21074 ---
all0.21332 11259 --
obs0.21332 11259 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.66 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å2-0 Å2-0 Å2
2--1.21 Å20 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 43 26 1288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.1941.9951760
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.345152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49124.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36815235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.657154
X-RAY DIFFRACTIONr_chiral_restr0.1380.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02966
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 34 -
Rwork0.283 714 -
obs--96.64 %

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