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

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Basic information

Entry
Database: PDB / ID: 5hlu
TitleX-ray crystal structure of met F43H/H64A sperm whale myoglobin in complex with nitric oxide
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / 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)17,8053
Polymers17,1591
Non-polymers6462
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-23 kcal/mol
Surface area7760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.690, 49.528, 77.598
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-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
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: 23916 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 14.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 21 / Rsym value: 0.073 / % possible all: 99.8

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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→41.75 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.863 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.062 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1594 1284 5.1 %RANDOM
Rwork0.14097 ---
obs0.14191 23916 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.5→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 45 285 1533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0191290
X-RAY DIFFRACTIONr_bond_other_d0.0010.021262
X-RAY DIFFRACTIONr_angle_refined_deg2.3562.0021745
X-RAY DIFFRACTIONr_angle_other_deg0.97432912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6965153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45724.44454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.315236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.732154
X-RAY DIFFRACTIONr_chiral_restr0.1620.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021427
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02293
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_it1.0180.742610
X-RAY DIFFRACTIONr_mcbond_other0.9530.737608
X-RAY DIFFRACTIONr_mcangle_it1.4021.109760
X-RAY DIFFRACTIONr_mcangle_other1.4181.113761
X-RAY DIFFRACTIONr_scbond_it2.8671.056680
X-RAY DIFFRACTIONr_scbond_other2.8691.057678
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3291.446984
X-RAY DIFFRACTIONr_long_range_B_refined6.5519.0271853
X-RAY DIFFRACTIONr_long_range_B_other5.6417.1921639
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
Rfree0.191 102 -
Rwork0.16 1684 -
obs--97.81 %

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