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- PDB-3nml: Sperm whale myoglobin mutant H64W carbonmonoxy-form -

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Basic information

Entry
Database: PDB / ID: 3nml
TitleSperm whale myoglobin mutant H64W carbonmonoxy-form
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / Myoglobin / ligand migration pathways
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsBirukou, I. / Soman, J. / Olson, J.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Blocking the gate to ligand entry in human hemoglobin.
Authors: Birukou, I. / Soman, J. / Olson, J.S.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.version
Revision 1.3Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3466
Polymers17,4131
Non-polymers9335
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.930, 46.960, 89.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myoglobin


Mass: 17413.225 Da / Num. of mol.: 1 / Mutation: H65W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): Phage resistant TB1 / 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 293 K / Method: batch method / pH: 9
Details: Protein solution (20mg/ml protein in 0.02m Tris-HCl ph9.0) mixed with mother liquor (3.2m ammonium sulphate, 0.05m tris-hcl, ph9.0) for final concentrations of 2.5m ammonium sulphate, Batch ...Details: Protein solution (20mg/ml protein in 0.02m Tris-HCl ph9.0) mixed with mother liquor (3.2m ammonium sulphate, 0.05m tris-hcl, ph9.0) for final concentrations of 2.5m ammonium sulphate, Batch Method, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 10, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→41.59 Å / Num. obs: 19145 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 3.71 % / Rmerge(I) obs: 0.041 / Χ2: 0.97 / Net I/σ(I): 19.7 / Scaling rejects: 537
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.68-1.743.20.1597573817880.8994.7
1.74-1.813.750.1388.3700818620.8898.1
1.81-1.893.740.138.6701618700.8898.8
1.89-1.993.690.1129.6702218860.8698.7
1.99-2.123.810.08513729419150.8499.7
2.12-2.283.80.0617.6729619140.8799.8
2.28-2.513.830.05122.2741819260.999.9
2.51-2.873.830.05720.9750119410.9499.8
2.87-3.623.80.03832.9758319781.0799.9
3.62-41.593.610.02951.6770420651.5199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
CNSrefinement
d*TREKdata scaling
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MBW

2mbw


Resolution: 1.68→22.711 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 16.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1909 10 %RANDOM
Rwork0.1658 ---
obs0.1689 19099 98.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.308 Å2 / ksol: 0.419 e/Å3
Displacement parametersBiso max: 132.35 Å2 / Biso mean: 20.653 Å2 / Biso min: 6.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.2507 Å2-0 Å2-0 Å2
2---0.9086 Å20 Å2
3----0.342 Å2
Refinement stepCycle: LAST / Resolution: 1.68→22.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 60 233 1522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191381
X-RAY DIFFRACTIONf_angle_d1.2421883
X-RAY DIFFRACTIONf_chiral_restr0.064191
X-RAY DIFFRACTIONf_plane_restr0.005234
X-RAY DIFFRACTIONf_dihedral_angle_d13.89508
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 (%)
1.68-1.72190.21211220.1551106122892
1.7219-1.76840.20031330.15051194132797
1.7684-1.82050.18711350.13911213134899
1.8205-1.87920.18421330.14971200133398
1.8792-1.94630.19561340.15271201133598
1.9463-2.02420.21031360.147612201356100
2.0242-2.11630.18151350.14031225136099
2.1163-2.22780.1611360.129112231359100
2.2278-2.36720.16031380.12212451383100
2.3672-2.54970.14541360.126812331369100
2.5497-2.80590.18231390.151912491388100
2.8059-3.2110.21661400.165612631403100
3.211-4.04180.17581410.141612691410100
4.0418-22.71350.16921510.17313491500100

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