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- PDB-1npg: MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITROSOETHANE -

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Basic information

Entry
Database: PDB / ID: 1npg
TitleMYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITROSOETHANE
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / HEME / OXYGEN STORAGE / NITRIC OXIDE / NITROSOETHANE / MYOGLOBIN / NITROSOALKANE / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / 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 / NITROSOETHANE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCopeland, D.M. / West, A.H. / Richter-Addo, G.B.
CitationJournal: Proteins / Year: 2003
Title: Crystal structures of ferrous horse heart myoglobin complexed with nitric oxide and nitrosoethane.
Authors: Copeland, D.M. / West, A.H. / Richter-Addo, G.B.
History
DepositionJan 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 16, 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_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.pdbx_dist_value / _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_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)17,8515
Polymers16,9841
Non-polymers8684
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.165, 28.706, 63.032
Angle α, β, γ (deg.)90.00, 106.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ANIMAL OXYGEN STORAGE / Source: (natural) Equus caballus (horse) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P68082
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-NOE / NITROSOETHANE


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.56 Å3/Da / Density % sol: 20.38 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: AMMONIUM SULFATE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
2100 mMTris-HCl1droppH7.4
33.4-4.0 Mammonium sulfate1drop
4100 mMTris-HCl1droppH7.4
53.1-3.3 Mammonium sulfate1reservoir
6100 mMTris-HCl1reservoirpH7.4

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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: Sep 11, 2002 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 23424 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.89 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 24.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 5.1 / % possible all: 98.2
Reflection
*PLUS
Num. obs: 13504 / Num. measured all: 39336
Reflection shell
*PLUS
% possible obs: 98.2 % / Num. unique obs: 1323 / Num. measured obs: 3655

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Processing

Software
NameClassification
d*TREKdata scaling
d*TREKdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DWR

1dwr


Resolution: 1.7→40 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 -10 %RANDOM
Rwork0.2 ---
all0.213 ---
obs0.2 23413 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.043 Å2 / ksol: 0.349798 e/Å3
Displacement parametersBiso mean: 16.4 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 57 169 1420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d16.5
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.022 /
Rfactor% reflection
Rfree0.37 10 %
Rwork0.378 -
obs-98.2 %
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.414
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
LS refinement shell
*PLUS
Rfactor Rfree: 0.412 / Rfactor Rwork: 0.418

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