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- PDB-7sli: Engineered sperm whale myoglobin-based carbene transferase MbBTIC-C2 -

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Basic information

Entry
Database: PDB / ID: 7sli
TitleEngineered sperm whale myoglobin-based carbene transferase MbBTIC-C2
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / METALLOPROTEIN / MYOGLOBIN / HEME / TRANSFERASE / OXYGEN TRANSPORT
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJenkins, J.L. / Vargas, D. / Ren, X. / Fasan, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM98628 United States
CitationJournal: To Be Published
Title: Enzymatic Strategy Towards the Construction of sp3-rich Complex Molecules Assisted by Computational Methods
Authors: Vargas, D. / Ren, X. / Jenkins, J.L. / Fasan, R.
History
DepositionOct 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)18,60810
Polymers17,2231
Non-polymers1,3859
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.440, 90.440, 45.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-206-

SO4

21A-520-

HOH

31A-537-

HOH

41A-546-

HOH

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Components

#1: Protein Myoglobin /


Mass: 17222.982 Da / Num. of mol.: 1 / Mutation: F43I,F46L,H64F,V68G,I107A, N122D
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 2.6 M Ammonium Sulfate, 20 mM tris-HCl pH 8.2, 0.1 mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→21.73 Å / Num. obs: 27689 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.976 / Rpim(I) all: 0.044 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 7 % / Mean I/σ(I) obs: 5.9 / Num. unique obs: 1053 / CC1/2: 0.97 / Rpim(I) all: 0.091 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
CrysalisProC171.41data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unpublished structure

Resolution: 2→20.23 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 17.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 1384 5 %
Rwork0.1428 26305 -
obs0.1453 27689 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.78 Å2 / Biso mean: 14.3581 Å2 / Biso min: 2.57 Å2
Refinement stepCycle: final / Resolution: 2→20.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 113 300 1597
Biso mean--21.52 23.62 -
Num. residues----152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.070.19021280.14272524265295
2.07-2.150.17981290.12962694282399
2.15-2.250.17611240.132226462770100
2.25-2.370.16861330.125526802813100
2.37-2.520.2051390.132526452784100
2.52-2.710.20471630.142725892752100
2.72-2.980.19781340.162926582792100
2.99-3.420.19741570.148126502807100
3.42-4.290.17171400.1262629276999
4.31-20.230.2151370.17372590272797

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