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- PDB-7l3y: Crystal structure of oxy-I107E CuB myoglobin (I107E L29H F43H spe... -

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Basic information

Entry
Database: PDB / ID: 7l3y
TitleCrystal structure of oxy-I107E CuB myoglobin (I107E L29H F43H sperm whale myoglobin; partial occupancy)
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / globin / oxidase / oxygen binding / oxygen reduction / OXIDOREDUCTASE
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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PEROXIDE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsPetrik, I. / Lu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM062211 United States
CitationJournal: Biochemistry / Year: 2021
Title: An Engineered Glutamate in Biosynthetic Models of Heme-Copper Oxidases Drives Complete Product Selectivity by Tuning the Hydrogen-Bonding Network.
Authors: Petrik, I.D. / Davydov, R. / Kahle, M. / Sandoval, B. / Dwaraknath, S. / Adelroth, P. / Hoffman, B. / Lu, Y.
History
DepositionDec 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0824
Polymers17,3981
Non-polymers6843
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.845, 46.982, 78.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Myoglobin


Mass: 17398.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 1.5-2.0 mM protein in 20 mM tris sulfate pH 8.0 buffer, mixed 1:1 with crystallization solution composed of 100 mM tris sulfate pH 8.6, 200 mM sodium acetate, and 30% w/v PEG 10000. After ...Details: 1.5-2.0 mM protein in 20 mM tris sulfate pH 8.0 buffer, mixed 1:1 with crystallization solution composed of 100 mM tris sulfate pH 8.6, 200 mM sodium acetate, and 30% w/v PEG 10000. After crystalization, soaked, under anaerobic conditions, in 20 mM dithionite for 10 minutes, and washed with anaerobic buffer. Reduced crystals were sealed in an air-tight bomb and pressurized at ~1500 psi O2 for up to 10 minutes. Crystals were harvested and cryocooled after a brief soak in 50% PEG 400 supersaturated with O2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.18→39.02 Å / Num. obs: 47352 / % possible obs: 97 % / Redundancy: 3.9 % / CC1/2: 1 / Rmerge(I) obs: 0.024 / Rpim(I) all: 0.013 / Rrim(I) all: 0.028 / Net I/σ(I): 31.7 / Num. measured all: 182510 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.18-1.22.10.216310715100.9020.1690.2754.163.4
6.47-39.0240.01714483600.9990.0090.01992.699.1

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Processing

Software
NameVersionClassification
PHENIX1.19rc7_4070refinement
Aimless0.5.12data scaling
PDB_EXTRACT3.27data extraction
XDSv2015-03-01data reduction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FWX

4fwx


Resolution: 1.18→39.02 Å / SU ML: 0.1094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.559
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1902 4119 4.77 %
Rwork0.1566 82228 -
obs0.1582 86347 92.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.26 Å2
Refinement stepCycle: LAST / Resolution: 1.18→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 46 297 1562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01271371
X-RAY DIFFRACTIONf_angle_d1.39671866
X-RAY DIFFRACTIONf_chiral_restr0.1015195
X-RAY DIFFRACTIONf_plane_restr0.0107232
X-RAY DIFFRACTIONf_dihedral_angle_d14.941533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.190.3196660.24081237X-RAY DIFFRACTION40.71
1.19-1.210.24041280.23112555X-RAY DIFFRACTION82.53
1.21-1.220.24911450.21592775X-RAY DIFFRACTION91.59
1.22-1.240.22981420.2082878X-RAY DIFFRACTION94.64
1.24-1.260.24581480.20082918X-RAY DIFFRACTION94.43
1.26-1.280.24131470.20222848X-RAY DIFFRACTION94.24
1.28-1.290.2481350.17822858X-RAY DIFFRACTION94.06
1.29-1.310.19311400.17262916X-RAY DIFFRACTION95.02
1.31-1.340.22331450.18512937X-RAY DIFFRACTION96.07
1.34-1.360.19111430.172907X-RAY DIFFRACTION94.63
1.36-1.380.21141430.16752947X-RAY DIFFRACTION96.05
1.38-1.410.19731480.16622954X-RAY DIFFRACTION97.73
1.41-1.440.20621500.16162979X-RAY DIFFRACTION96.72
1.44-1.470.18361520.16212968X-RAY DIFFRACTION96.8
1.47-1.50.17531410.14772942X-RAY DIFFRACTION96.95
1.5-1.540.17151400.15182937X-RAY DIFFRACTION95.35
1.54-1.580.17771500.14852888X-RAY DIFFRACTION94.88
1.58-1.630.19331480.14122971X-RAY DIFFRACTION97.5
1.63-1.680.14831500.14762979X-RAY DIFFRACTION97.08
1.68-1.740.19641520.14922992X-RAY DIFFRACTION97.28
1.74-1.810.17121480.15712933X-RAY DIFFRACTION96.52
1.81-1.90.16521450.15522918X-RAY DIFFRACTION96.17
1.9-20.16021470.15362770X-RAY DIFFRACTION90.93
2-2.120.17951630.14512865X-RAY DIFFRACTION94.15
2.12-2.280.17971470.15082843X-RAY DIFFRACTION93.79
2.28-2.510.19631450.1572928X-RAY DIFFRACTION95.43
2.51-2.880.19731360.162770X-RAY DIFFRACTION90.78
2.88-3.630.20971270.14842935X-RAY DIFFRACTION95.21
3.63-39.020.18371480.14622880X-RAY DIFFRACTION94.62

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