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- PDB-1do4: CARBONMONOXY-MYOGLOBIN (MUTANT L29W) AFTER PHOTOLYSIS AT T<180K -

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Basic information

Entry
Database: PDB / ID: 1do4
TitleCARBONMONOXY-MYOGLOBIN (MUTANT L29W) AFTER PHOTOLYSIS AT T<180K
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE/TRANSPORT / HEME / RESPIRATORY PROTEIN / PHOTOLYSED MYOGLOBIN / LIGAND MIGRATION / OXYGEN STORAGE-TRANSPORT COMPLEX
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
trehalose / CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsOstermann, A. / Waschipky, R. / Parak, F.G. / Nienhaus, G.U.
CitationJournal: Nature / Year: 2000
Title: Ligand binding and conformational motions in myoglobin.
Authors: Ostermann, A. / Waschipky, R. / Parak, F.G. / Nienhaus, G.U.
History
DepositionDec 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 2.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details

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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)18,6456
Polymers17,4661
Non-polymers1,1795
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.430, 90.430, 45.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-246-

HOH

21A-252-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein MYOGLOBIN


Mass: 17466.225 Da / Num. of mol.: 1 / Mutation: M0(FME), L29W, D122N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 193 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 59.76 %
Crystal growTemperature: 292 K / Method: batch crystallization / pH: 8.5
Details: CRYSTALS WERE GROWN IN 2.5M AMMONIUM SULFATE SOLUTION, BUFFERED WITH 20MM TRIS/ HCL TO PH 8.5. THE CRYSTALLIZATION SOLUTION WAS REPLACED IN STEPS AGAINST A SOLUTION CONTAINING 2.5M AMMONIUM ...Details: CRYSTALS WERE GROWN IN 2.5M AMMONIUM SULFATE SOLUTION, BUFFERED WITH 20MM TRIS/ HCL TO PH 8.5. THE CRYSTALLIZATION SOLUTION WAS REPLACED IN STEPS AGAINST A SOLUTION CONTAINING 2.5M AMMONIUM SULFATE, 20MM TRIS, 300MG/ML TREHALOSE AT PH 8.5., BATCH CRYSTALLIZATION, temperature 292K
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mML29W MbCO11
275 %glycerol11
325 %(v/v)potassium phosphate11
42.5 Mammonium sulfate12
6300 mg/mltrehalose12
5Tris-HCl12

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 15, 1998 / Details: graphite
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. obs: 22384 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 4.3 / % possible all: 86.4
Reflection
*PLUS
Num. measured all: 140474 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 86.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
SAINT(SIEMENS)data reduction
SAINT(SIEMENS)data scaling
CCP4(AGROVATAdata scaling
TRUNCATEdata scaling
RefinementStarting model: 1DO1

1do1


Resolution: 1.7→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: free r / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: NO ANGLE RESTRAINTS WERE USED FOR THE HIS 93 WITH RESPECT TO THE IRON ATOM. BOND RESTRAINTS FOR THE HIS 93 AND FOR THE FOUR PYRROLE NITROGEN ATOMS TO THE IRON ATOM WERE WEAKENED FROM THE ...Details: NO ANGLE RESTRAINTS WERE USED FOR THE HIS 93 WITH RESPECT TO THE IRON ATOM. BOND RESTRAINTS FOR THE HIS 93 AND FOR THE FOUR PYRROLE NITROGEN ATOMS TO THE IRON ATOM WERE WEAKENED FROM THE STANDARD X-PLOR VALUES (PARAM19X.HEME). THERE IS NEARLY NO ELECTRON DENSITY FOR THE N-FORMYL-MET. THIS RESIDUE WAS NOT INCLUDED INTO THE MODEL. ELECTRON DENSITY FEATURES CLOSE TO THIS SITE WERE MODELED BY WATER MOLECULES. ONE TREHALOSE MOLECULE IS BOUND TO THE SURFACE OF THE MYOGLOBIN MOLECULE. THE WATER MOLECULES NUMBER 246 AND 252 ARE ON OR CLOSE TO SPECIAL POSITIONS. THE ORIENTATION OF THE CO-MOLECULE CANNOT BE DETERMINED FROM THE DATA AND WAS ARBITRARILY ASSIGNED. ELECTRON DENSITY FOR THE CO-MOLECULE IS FOUND IN A CAVITY CLOSE TO TRP29
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2190 -RANDOM
Rwork0.184 ---
all0.186 22148 --
obs0.186 22148 96 %-
Refine analyzeLuzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 78 189 1490
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.273 243 -
Rwork0.24 2286 -
obs--87.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7 Å / σ(F): 0 / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.273 / Rfactor Rwork: 0.24

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