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- PDB-5d5r: Horse-heart myoglobin - deoxy state -

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Basic information

Entry
Database: PDB / ID: 5d5r
TitleHorse-heart myoglobin - deoxy state
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / myoglobin / heme protein
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 / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBarends, T. / Schlichting, I.
CitationJournal: Science / Year: 2015
Title: Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation.
Authors: Barends, T.R. / Foucar, L. / Ardevol, A. / Nass, K. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. / Heinz, M. / Hoffmann, M.C. / Kofinger, J. / Koglin, J. ...Authors: Barends, T.R. / Foucar, L. / Ardevol, A. / Nass, K. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. / Heinz, M. / Hoffmann, M.C. / Kofinger, J. / Koglin, J.E. / Kovacsova, G. / Liang, M. / Milathianaki, D. / Lemke, H.T. / Reinstein, J. / Roome, C.M. / Shoeman, R.L. / Williams, G.J. / Burghardt, I. / Hummer, G. / Boutet, S. / Schlichting, I.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)17,5432
Polymers16,9261
Non-polymers6161
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-20 kcal/mol
Surface area7760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.600, 28.800, 35.600
Angle α, β, γ (deg.)90.00, 106.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 16926.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P68082
#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.: 120 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.5 M ammonium sulphate, 0.1 M Tris-HCl pH 7.4

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→35 Å / Num. obs: 16486 / % possible obs: 96.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.3
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.9 / % possible all: 87.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CMV

5cmv


Resolution: 1.6→34.213 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 825 5 %
Rwork0.1723 --
obs0.174 16486 93.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→34.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 43 120 1357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071271
X-RAY DIFFRACTIONf_angle_d1.1141722
X-RAY DIFFRACTIONf_dihedral_angle_d15.705457
X-RAY DIFFRACTIONf_chiral_restr0.038178
X-RAY DIFFRACTIONf_plane_restr0.004214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5719-1.67040.29041070.23971983X-RAY DIFFRACTION72
1.6704-1.79930.23531340.21472625X-RAY DIFFRACTION95
1.7993-1.98040.25131460.18332728X-RAY DIFFRACTION99
1.9804-2.26690.20851440.16632750X-RAY DIFFRACTION99
2.2669-2.85580.20591470.17522776X-RAY DIFFRACTION100
2.8558-34.22150.17881470.15652799X-RAY DIFFRACTION98

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