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- PDB-5hlx: X-ray crystal structure of met F43H/H64A sperm whale myoglobin in... -

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Basic information

Entry
Database: PDB / ID: 5hlx
TitleX-ray crystal structure of met F43H/H64A sperm whale myoglobin in complex with nitrite
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 / NITRITE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsYuan, H.
CitationJournal: Nitric Oxide / Year: 2016
Title: Regulating the nitrite reductase activity of myoglobin by redesigning the heme active center
Authors: Wu, L.B. / Yuan, H. / Gao, S.Q. / You, Y. / Nie, C.M. / Wen, G.B. / Lin, Y.W. / Tan, X.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Nov 8, 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)17,8674
Polymers17,1591
Non-polymers7083
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-19 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.701, 49.545, 77.588
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: 17158.855 Da / Num. of mol.: 1 / Fragment: UNP residues 2-154 / Mutation: F43H/H64A
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-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 44.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30%(w/v) Polyethylene glycol 8,000, 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH 6.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.988 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jan 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 25250 / % possible obs: 99.8 % / Redundancy: 6.4 % / Net I/σ(I): 20.08
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 20.1 / Rsym value: 0.099 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data scaling
MOLREPphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OF9

4of9


Resolution: 1.5→35.37 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.955 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17332 1286 5.1 %RANDOM
Rwork0.1479 ---
obs0.14921 23910 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.775 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å20 Å2
2--0.47 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.5→35.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 49 286 1545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0191298
X-RAY DIFFRACTIONr_bond_other_d0.0020.021278
X-RAY DIFFRACTIONr_angle_refined_deg2.3652.0031756
X-RAY DIFFRACTIONr_angle_other_deg1.04732948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7465154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5124.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36615239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.886154
X-RAY DIFFRACTIONr_chiral_restr0.1730.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021430
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02294
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_it1.1470.801613
X-RAY DIFFRACTIONr_mcbond_other1.1320.798612
X-RAY DIFFRACTIONr_mcangle_it1.7121.197765
X-RAY DIFFRACTIONr_mcangle_other1.7231.2766
X-RAY DIFFRACTIONr_scbond_it2.7331.112685
X-RAY DIFFRACTIONr_scbond_other2.7391.106679
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0541.523988
X-RAY DIFFRACTIONr_long_range_B_refined6.1739.4811885
X-RAY DIFFRACTIONr_long_range_B_other5.5567.7791674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 84 -
Rwork0.178 1732 -
obs--99.23 %

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