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- PDB-1npf: MYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITRIC OXIDE -

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Basic information

Entry
Database: PDB / ID: 1npf
TitleMYOGLOBIN (HORSE HEART) WILD-TYPE COMPLEXED WITH NITRIC OXIDE
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / HEME / OXYGEN STORAGE / NITRIC OXIDE / MYOGLOBIN / NITROSYL / NO / NITROGEN MONOXIDE / 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 / NITRIC OXIDE / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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)17,8225
Polymers16,9841
Non-polymers8394
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.437, 28.728, 62.976
Angle α, β, γ (deg.)90.00, 105.81, 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-NO / NITRIC OXIDE / Nitrogen monoxide


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


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.63 Å3/Da / Density % sol: 23.76 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: AMMONIUM SULFATE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Chu, K., (2000) Nature, 403, 921.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
21.7-1.8 Mammonium sulfate1drop
30.1 MTris-HCl1drop
43.4-3.6 Mammonium sulfate1reservoir
50.1 MTris-HCl1reservoir

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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: Nov 6, 2002 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 17516 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 3.4 / % possible all: 91.1
Reflection
*PLUS
Num. measured all: 34504
Reflection shell
*PLUS
% possible obs: 91.1 % / Num. unique obs: 1687 / Num. measured obs: 3332

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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: 1.9→40 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -10 %RANDOM
Rwork0.199 ---
all0.217 17516 --
obs0.199 17516 93.1 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 17.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 55 118 1367
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d64.3
X-RAY DIFFRACTIONc_improper_angle_d1.56
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.021 /
Rfactor% reflection
Rfree0.366 10 %
Rwork0.291 -
obs-91.1 %
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.055
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg64.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.56
LS refinement shell
*PLUS
Rfactor Rfree: 0.384 / Rfactor Rwork: 0.365

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