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- PDB-4lpi: A sperm whale myoglobin double mutant L29H/F43Y Mb with a distal ... -

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Basic information

Entry
Database: PDB / ID: 4lpi
TitleA sperm whale myoglobin double mutant L29H/F43Y Mb with a distal hydrogen-bonding network
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Enzyme Function Initiative / distal heme hydrogen-bonding network / Nitrite redutase
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / 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: 1.36 Å
AuthorsLin, Y.
CitationJournal: Dalton Trans / Year: 2015
Title: How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin
Authors: Yan, D.J. / Yuan, H. / Li, W. / Xiang, Y. / He, B. / Nie, C.M. / Wen, G.B. / Lin, Y.W. / Tan, X.
History
DepositionJul 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 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

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0242
Polymers17,4071
Non-polymers6161
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.884, 48.184, 78.458
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: 17407.137 Da / Num. of mol.: 1 / Mutation: L29H/F43Y
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate, 30% w/v Polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.36→35.55 Å / Num. obs: 32680 / % possible obs: 7.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIX1.7.1_743refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IT8

4it8


Resolution: 1.36→35.55 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8944 / SU ML: 0.3 / σ(F): 0.23 / Phase error: 17.13 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1991 2000 6.12 %
Rwork0.1801 --
obs0.1812 32680 98.22 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.459 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso max: 47.56 Å2 / Biso mean: 15.3793 Å2 / Biso min: 5.09 Å2
Baniso -1Baniso -2Baniso -3
1--1.6534 Å2-0 Å20 Å2
2---0.3422 Å2-0 Å2
3---1.9956 Å2
Refinement stepCycle: LAST / Resolution: 1.36→35.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 43 199 1461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071296
X-RAY DIFFRACTIONf_angle_d1.1321756
X-RAY DIFFRACTIONf_dihedral_angle_d14.985469
X-RAY DIFFRACTIONf_chiral_restr0.072181
X-RAY DIFFRACTIONf_plane_restr0.005217
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3595-1.39350.23581350.19012062219794
1.3935-1.43110.20631360.18932099223596
1.4311-1.47320.22071390.17692125226497
1.4732-1.52080.18851390.16632146228597
1.5208-1.57520.17651410.16722142228398
1.5752-1.63820.17851400.16652166230698
1.6382-1.71280.19571430.17232172231598
1.7128-1.80310.19361420.17532191233399
1.8031-1.9160.19631440.17272207235199
1.916-2.0640.19311430.173322072350100
2.064-2.27160.20061470.171122422389100
2.2716-2.60030.17971470.178922572404100
2.6003-3.27570.19511480.187922772425100
3.2757-35.5660.21731560.190923872543100

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