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- PDB-1lht: LOGGERHEAD SEA TURTLE MYOGLOBIN (CYANO-MET) -

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Basic information

Entry
Database: PDB / ID: 1lht
TitleLOGGERHEAD SEA TURTLE MYOGLOBIN (CYANO-MET)
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesCaretta caretta (Loggerhead turtle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsNardini, M. / Tarricone, C. / Lania, A. / Desideri, A. / De Sanctis, G. / Coletta, M. / Petruzzelli, R. / Ascenzi, P. / Coda, A. / Bolognesi, M.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Reptile heme protein structure: X-ray crystallographic study of the aquo-met and cyano-met derivatives of the loggerhead sea turtle (Caretta caretta) myoglobin at 2.0 A resolution.
Authors: Nardini, M. / Tarricone, C. / Rizzi, M. / Lania, A. / Desideri, A. / De Sanctis, G. / Coletta, M. / Petruzzelli, R. / Ascenzi, P. / Coda, A. / Bolognesi, M.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: X-ray crystal structure of ferric Aplysia limacina myoglobin in different liganded states.
Authors: Conti, E. / Moser, C. / Rizzi, M. / Mattevi, A. / Lionetti, C. / Coda, A. / Ascenzi, P. / Brunori, M. / Bolognesi, M.
#2: Journal: Biochem.Mol.Biol.Int. / Year: 1993
Title: Structural Studies on the Loggerhead Sea Turtle (Caretta Caretta) Myoglobin
Authors: Petruzzelli, R. / Aureli, G. / Casale, E. / Nardini, M. / Rizzi, M. / Ascenzi, P. / Coletta, M. / De Sanctis, G. / Desideri, A. / Galtieri, A. / Bolognesi, M.
History
DepositionFeb 1, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Feb 15, 2017Group: Database references
Revision 1.5Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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

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Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0633
Polymers17,4211
Non-polymers6432
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.570, 61.270, 75.290
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 MYOGLOBIN /


Mass: 17420.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caretta caretta (Loggerhead turtle) / References: UniProt: P56208
#2: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein11
23.2 Mammonium sulfate12
30.05 MTris-HCl12

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 1, 1994
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 9759 / % possible obs: 81 % / Observed criterion σ(I): 3 / Redundancy: 4.5 %
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 44352 / Rmerge(I) obs: 0.0497

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
TNTrefinement
X-PLOR3.1refinement
MOSFLMdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→15 Å / σ(F): 3 /
RfactorNum. reflection
obs0.178 9759
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 45 68 1261
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg3.03

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