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- PDB-5ilr: H64Q sperm whale myoglobin with a Fe-chlorophenyl moiety -

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Basic information

Entry
Database: PDB / ID: 5ilr
TitleH64Q sperm whale myoglobin with a Fe-chlorophenyl moiety
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Iron / Organometallic / Bioorganometallic / Heme / Myoglobin / Sigma-aryl / Hydrazine / Arylhydrazine / Phenylhydrazine / Iron-carbon / 3-methylphenylhydrazine / meta-tolylhydrazine / 4-chlorophenylhydrazine / para-chlorophenylhydrazine
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 domain 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: 1.87 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 / Category: pdbx_audit_support / 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)18,4636
Polymers17,3551
Non-polymers1,1085
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.361, 30.315, 64.368
Angle α, β, γ (deg.)90.000, 105.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 17355.145 Da / Num. of mol.: 1 / Mutation: H64Q
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) / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.9 Å3/Da / Density % sol: 35.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM Tris-HCl pH 7.4, 1 mM EDTA, 3.0 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: Mar 24, 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: 1.87→50 Å / Num. obs: 10786 / % possible obs: 99.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.027 / Rrim(I) all: 0.053 / Χ2: 0.757 / Net I/av σ(I): 28.411 / Net I/σ(I): 11.6 / Num. measured all: 40427
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.87-1.930.216198.2
1.9-1.943.30.184199.8
1.94-1.973.60.194199.8
1.97-2.013.60.158199.4
2.01-2.063.60.153199.2
2.06-2.113.80.117199.6
2.11-2.163.80.098199.3
2.16-2.223.90.082199.6
2.22-2.2840.086199.4
2.28-2.363.90.083199.6
2.36-2.4440.061199.6
2.44-2.5440.061199.5
2.54-2.653.90.056199.4
2.65-2.7940.052198.9
2.79-2.973.90.045199.3
2.97-3.240.044199.1
3.2-3.523.90.032198.9
3.52-4.033.80.029198.6
4.03-5.073.70.029197.7
5.07-503.30.024196.5

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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: 1.87→33.16 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.718 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.032
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY ONLY ANISOTROPIC REFINEMENT OF HEME IRON
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 519 4.8 %RANDOM
Rwork0.1637 ---
obs0.166 10255 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 59.28 Å2 / Biso mean: 20.368 Å2 / Biso min: 7.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0.65 Å2
2--0.09 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.87→33.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1202 0 71 104 1377
Biso mean--27.22 27.7 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021331
X-RAY DIFFRACTIONr_bond_other_d0.0030.021297
X-RAY DIFFRACTIONr_angle_refined_deg2.032.0641813
X-RAY DIFFRACTIONr_angle_other_deg1.10732987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2775158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49424.73757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71215242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.449154
X-RAY DIFFRACTIONr_chiral_restr0.1290.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021470
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02306
X-RAY DIFFRACTIONr_mcbond_it1.8071.675611
X-RAY DIFFRACTIONr_mcbond_other1.7361.671610
X-RAY DIFFRACTIONr_mcangle_it2.4782.499764
X-RAY DIFFRACTIONr_sphericity_bonded6.89551
LS refinement shellResolution: 1.868→1.916 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 38 -
Rwork0.173 754 -
all-792 -
obs--97.18 %

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