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

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Basic information

Entry
Database: PDB / ID: 4fwz
TitleAquoferric CuB myoglobin (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. / 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 1.1Nov 14, 2012Group: Refinement description
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)17,8672
Polymers17,2511
Non-polymers6161
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)39.737, 47.682, 77.543
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: 17250.914 Da / Num. of mol.: 1 / Mutation: L29H, 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.: 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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: CuBMb (2.2 mM) in 20 mM tris(hydroxymethyl)aminomethane (tris) pH 8 (pH adjusted H2SO4), was mixed 1:1 with well buffer (0.2 M sodium acetate, 0.1 M tris hydrochloride pH 8.5, with 30% ...Details: CuBMb (2.2 mM) in 20 mM tris(hydroxymethyl)aminomethane (tris) pH 8 (pH adjusted H2SO4), was mixed 1:1 with well buffer (0.2 M sodium acetate, 0.1 M tris hydrochloride pH 8.5, with 30% polyethylene glycol 4000) 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: X12B / Wavelength: 0.894 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.894 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 12087 / Num. obs: 12087 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 40.1
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 9.8 / % possible all: 98.7

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Processing

Software
NameClassification
CBASSdata collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: SHELX DEFAULT
RfactorNum. reflectionSelection details
all0.275 11305 -
obs0.204 11305 -
Rfree-599 RANDOM
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 43 144 1405
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d1.842

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