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- PDB-1dti: Recombinant sperm whale myoglobin h97d, d122n mutant (met) -

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Basic information

Entry
Database: PDB / ID: 1dti
TitleRecombinant sperm whale myoglobin h97d, d122n mutant (met)
ComponentsPROTEIN (MYOGLOBIN)
KeywordsOXYGEN STORAGE/TRANSPORT / HEME / OXYGEN TRANSPORT / MUSCLE PROTEIN / 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-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 / DIFFERENCE FOURIER / Resolution: 1.7 Å
AuthorsLiong, E.C. / Phillips Jr., G.N.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Waterproofing the heme pocket. Role of proximal amino acid side chains in preventing hemin loss from myoglobin.
Authors: Liong, E.C. / Dou, Y. / Scott, E.E. / Olson, J.S. / Phillips Jr., G.N.
History
DepositionJan 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 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
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 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

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Assembly

Deposited unit
A: PROTEIN (MYOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9592
Polymers17,3421
Non-polymers6161
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.163, 40.002, 80.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (MYOGLOBIN)


Mass: 17342.104 Da / Num. of mol.: 1 / Mutation: H97D, 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: 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.: 80 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.6-3.0 M (NH4)2SO4, 20 MM TRIS, 1 MM EDTA, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
PH range low: 9 / PH range high: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
22.4-3.0 Mammonium sulfate1drop
320 mMTris-HCl1drop
41 mMEDTA1drop
52.4-3.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 24, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 17916 / % possible obs: 98 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.044
Reflection
*PLUS
Num. obs: 17917 / Num. measured all: 66693

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Processing

Software
NameClassification
XDSdata reduction
X-PLORmodel building
SHELXL-97refinement
XDSdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1MBW

1mbw
PDB Unreleased entry


Resolution: 1.7→5 Å / Num. parameters: 543 / Num. restraintsaints: 541 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1523 9 %RANDOM
all0.182 15394 --
obs0.183 15394 89.6 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1357
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 44 79 1346
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0.006
X-RAY DIFFRACTIONs_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.081
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.227 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.1
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg22
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.4

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