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- PDB-2nx0: Ferrous nitrosyl blackfin tuna myoglobin -

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Basic information

Entry
Database: PDB / ID: 2nx0
TitleFerrous nitrosyl blackfin tuna myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / myoglobin / NO / nitric oxide / ferrous nitrosyl / OXYGEN STORAGE-TRANSPORT COMPLEX
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
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Myoglobin / Myoglobin
Similarity search - Component
Biological speciesThunnus atlanticus (blackfin tuna)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsSchreiter, E.R. / Rodriguez, M.M. / Weichsel, A. / Montfort, W.R. / Bonaventura, J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: S-nitrosylation-induced conformational change in blackfin tuna myoglobin.
Authors: Schreiter, E.R. / Rodriguez, M.M. / Weichsel, A. / Montfort, W.R. / Bonaventura, J.
History
DepositionNov 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 3, 2020Group: Database references / Derived calculations / Source and taxonomy
Category: entity_src_nat / struct_conn ...entity_src_nat / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num ..._entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num
Revision 1.4Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2794
Polymers15,5361
Non-polymers7433
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.520, 51.530, 38.060
Angle α, β, γ (deg.)90.00, 105.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin /


Mass: 15536.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thunnus atlanticus (blackfin tuna) / References: UniProt: H3JQV6, UniProt: P68190*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M potassium/sodium tartrate, 0.1 M sodium citrate, 2.0 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.95→22 Å / Num. obs: 79652 / % possible obs: 98.7 % / Redundancy: 9.87 % / Rsym value: 0.089 / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MYT

1myt


Resolution: 0.95→21.81 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.729 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17805 4006 5 %RANDOM
Rwork0.15558 ---
all0.15673 77151 --
obs0.15673 75608 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.015 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.03 Å2
2--0.14 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 0.95→21.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1231 0 55 253 1539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221325
X-RAY DIFFRACTIONr_bond_other_d0.0010.02880
X-RAY DIFFRACTIONr_angle_refined_deg1.7282.0861820
X-RAY DIFFRACTIONr_angle_other_deg1.24232187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.095176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98725.65246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10715238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.033153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021518
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02236
X-RAY DIFFRACTIONr_nbd_refined0.2550.2392
X-RAY DIFFRACTIONr_nbd_other0.1880.21008
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2709
X-RAY DIFFRACTIONr_nbtor_other0.0950.2581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2177
X-RAY DIFFRACTIONr_metal_ion_refined0.2620.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1880.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.248
X-RAY DIFFRACTIONr_mcbond_it1.741.51071
X-RAY DIFFRACTIONr_mcbond_other0.8851.5333
X-RAY DIFFRACTIONr_mcangle_it2.05321323
X-RAY DIFFRACTIONr_scbond_it3.1673588
X-RAY DIFFRACTIONr_scangle_it4.064.5495
X-RAY DIFFRACTIONr_rigid_bond_restr1.53532655
X-RAY DIFFRACTIONr_sphericity_free8.9793255
X-RAY DIFFRACTIONr_sphericity_bonded5.35132164
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 279 -
Rwork0.232 5551 -
obs--98.76 %

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