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- PDB-5zeo: X-ray structure of sperm whale V21C/V66C/F46S myoglobin mutant wi... -

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Basic information

Entry
Database: PDB / ID: 5zeo
TitleX-ray structure of sperm whale V21C/V66C/F46S myoglobin mutant with an intramolecular disulfide bond
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / myoglobin / sperm whale
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: 1.77 Å
AuthorsYuan, H.
CitationJournal: Chem. Commun. (Camb.) / Year: 2018
Title: Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin
Authors: Yin, L.L. / Yuan, H. / Du, K.J. / He, B. / Gao, S.Q. / Wen, G.B. / Tan, X. / Lin, Y.W.
History
DepositionFeb 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 9, 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)17,7992
Polymers17,1831
Non-polymers6161
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-18 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.566, 47.351, 79.111
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: 17182.879 Da / Num. of mol.: 1 / Fragment: UNP residues 2-154 / Mutation: V21C, P46S, V66C
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30%(w/v) Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.77→40.63 Å / Num. obs: 15020 / % possible obs: 99.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 23.05
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 5.33 / Num. unique obs: 725 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HLX

5hlx


Resolution: 1.77→40.63 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2655 1496 10 %
Rwork0.2228 --
obs-15020 99.4 %
Refinement stepCycle: LAST / Resolution: 1.77→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 43 175 1428

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