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- PDB-5ilm: H64A sperm whale myoglobin with a Fe-chlorophenyl moiety -

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Basic information

Entry
Database: PDB / ID: 5ilm
TitleH64A sperm whale myoglobin with a Fe-chlorophenyl moiety
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Bioorganometallic / Heme / Sigma-aryl / Hydrazine / Arylhydrazine / Phenylhydrazine / Iron-carbon / 3-methylphenylhydrazine / meta-tolylhydrazine / 4-chlorophenylhydrazine / para-chlorophenylhydrazine
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
Chem-4HE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
Model detailsThis stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale ...This stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale myoglobin ferric H64A and N-hydroxyamphetamine.
AuthorsWang, B. / Thomas, L.M. / Richter-Addo, G.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1213674 United States
CitationJournal: J. Inorg. Biochem. / Year: 2016
Title: Organometallic myoglobins: Formation of Fe-carbon bonds and distal pocket effects on aryl ligand conformations.
Authors: Wang, B. / Thomas, L.M. / Richter-Addo, G.B.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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)18,6919
Polymers17,2981
Non-polymers1,3938
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.599, 90.599, 45.121
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-205-

SO4

21A-471-

HOH

31A-496-

HOH

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Components

#1: Protein Myoglobin /


Mass: 17298.094 Da / Num. of mol.: 1 / Mutation: H64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02185
#2: Chemical ChemComp-4HE / (4-chlorophenyl)[3,3'-(7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)di(propanoato)(2-)]iron


Mass: 728.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H36ClFeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsD123N CONFLICT EXISTS IN UNP ENTRY P02185

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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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 9
Details: 100 mM Tris-HCl pH 9.0, 1 mM EDTA, 2.3 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 19, 2014 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 23456 / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.064 / Net I/av σ(I): 34.878 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.7-1.736.20.4741100
1.73-1.767.10.4581100
1.76-1.798.30.4091100
1.79-1.838.70.3481100
1.83-1.878.90.2941100
1.87-1.919.20.2651100
1.91-1.969.50.2111100
1.96-2.029.70.1681100
2.02-2.07100.1411100
2.07-2.1410.10.1121100
2.14-2.22100.0971100
2.22-2.31100.0851100
2.31-2.41100.0781100
2.41-2.54100.0741100
2.54-2.79.90.0661100
2.7-2.919.80.0581100
2.91-3.29.60.0481100
3.2-3.669.10.0381100
3.66-4.618.40.0341100
4.61-507.50.023199.8

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Processing

Software
NameVersionClassification
HKL-3000phasing
PHASER2.5.2phasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
HKL-3000data collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MBW

2mbw


Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.634 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.088
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 1117 4.8 %RANDOM
Rwork0.1519 ---
obs0.1539 22177 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.86 Å2 / Biso mean: 17.412 Å2 / Biso min: 5.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 87 225 1524
Biso mean--25.07 29.9 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021372
X-RAY DIFFRACTIONr_bond_other_d0.0030.021331
X-RAY DIFFRACTIONr_angle_refined_deg2.4182.0751871
X-RAY DIFFRACTIONr_angle_other_deg1.1433069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.045164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11224.3158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38915247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.276155
X-RAY DIFFRACTIONr_chiral_restr0.1340.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021503
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02312
X-RAY DIFFRACTIONr_mcbond_it1.4811.288623
X-RAY DIFFRACTIONr_mcbond_other1.4671.287622
X-RAY DIFFRACTIONr_mcangle_it2.0851.923780
X-RAY DIFFRACTIONr_rigid_bond_restr6.184312
X-RAY DIFFRACTIONr_sphericity_bonded20.282514
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 56 -
Rwork0.19 1676 -
all-1732 -
obs--99.94 %

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