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- PDB-3h58: Myoglobin Cavity Mutant H64LV68N Met form -

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Basic information

Entry
Database: PDB / ID: 3h58
TitleMyoglobin Cavity Mutant H64LV68N Met form
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / OXYGEN TRANSPORT / Myoglobin / active site hydration / ligand entry and exit / oxygen storage and transport / Heme / Iron / Metal-binding / Muscle protein / Transport
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
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsSoman, J. / Olson, J.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Optical detection of disordered water within a protein cavity.
Authors: Goldbeck, R.A. / Pillsbury, M.L. / Jensen, R.A. / Mendoza, J.L. / Nguyen, R.L. / Olson, J.S. / Soman, J. / Kliger, D.S. / Esquerra, R.M.
History
DepositionApr 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Sep 6, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9722
Polymers17,3551
Non-polymers6161
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.130, 90.130, 45.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Myoglobin


Mass: 17355.146 Da / Num. of mol.: 1 / Mutation: H64L, V68N, D122N
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
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 IV++ / Detector: IMAGE PLATE / Date: Apr 12, 2008
RadiationMonochromator: Multilayer / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→39.03 Å / Num. all: 31355 / Num. obs: 26335 / % possible obs: 84 % / Observed criterion σ(I): 3 / Redundancy: 2.62 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.035 / Χ2: 0.85 / Net I/σ(I): 18.9 / Scaling rejects: 522
Reflection shellResolution: 1.54→1.59 Å / Redundancy: 1.04 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 3 / Num. measured all: 580 / Num. unique all: 546 / Χ2: 2.8 / % possible all: 17.4

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata processing
CNS1.1refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2mbw

2mbw


Resolution: 1.8→39.03 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.871 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 953 4.9 %random
Rwork0.196 ---
all-19639 --
obs-19536 99.5 %-
Solvent computationBsol: 60.01 Å2
Displacement parametersBiso max: 98.42 Å2 / Biso mean: 17.789 Å2 / Biso min: 4.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.295 Å2-1.969 Å20 Å2
2---0.295 Å20 Å2
3---0.591 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 43 293 1560
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.4
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.208 151 -
Rwork0.201 --
obs-3036 98.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2CVheme.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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