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- PDB-1dxc: CO complex of Myoglobin Mb-YQR at 100K -

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Basic information

Entry
Database: PDB / ID: 1dxc
TitleCO complex of Myoglobin Mb-YQR at 100K
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE / CO COMPLEX / RESPIRATORY PROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPHYSETER CATODON (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBrunori, M. / Vallone, B. / Cutruzzola, F. / Travaglini-Allocatelli, C. / Berendzen, J. / Chu, K. / Sweet, R.M. / Schlichting, I.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The Role of Cavities in Protein Dynamics: Crystal Structure of a Novel Photolytic Intermediate of Myoglobin
Authors: Brunori, M. / Vallone, B. / Cutruzzola, F. / Travaglini-Allocatelli, C. / Berendzen, J. / Chu, K. / Sweet, R.M. / Schlichting, I.
#1: Journal: Biophys.J. / Year: 1999
Title: Structural Dynamics of Liganddiffusion in the Protein Matrix: A Study on a New Myoglobin Mutant Y (B10) Q(E7) R(E10)
Authors: Brunori, M. / Cutruzzola, F. / Savino, C. / Travaglini-Allocatelli, C. / Vallone, B. / Gibson, Q.H.
#2: Journal: Nature / Year: 1994
Title: Crystal Structure of Photolysed Carbonmonoxy-Myoglobin
Authors: Schlichting, I. / Berendzen, J. / Juniorsweet, R.M.G.N.P.
#3: Journal: Proteins: Struct.,Funct., Genet. / Year: 1990
Title: Crystal Structure of Myoglobin from a Synthetic Gene
Authors: Juniorarduini, R.M.G.N.P. / Springer, B.A. / Sligar, S.G.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: High-Level Expression of Sperm Whale Myoglobin in Escherichia Coli
Authors: Springer, B.A. / Sligar, S.G.
History
DepositionJan 3, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2000Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Nov 27, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)18,3946
Polymers17,4611
Non-polymers9335
Water4,648258
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.610, 90.610, 45.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-315-

SO4

DetailsIN THIS SPACE GROUP THERE IS A STRONG 3 -FOLD CRYSTAL PACKINGOF THE MYOGLOBIN MOLECULE INVOLVING SYMMETRY OPERATIONS,(X,Y,Z), (1.0-X+ Y,1.0-X,Z), AND (1.0-Y,X-Y,Z). THE SO4MOLECULE 315A SITS CLOSE TO THE 3-FOLD AXIS.

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Components

#1: Protein MYOGLOBIN


Mass: 17461.250 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: HEME BOUND TO HIS-93, CO BOUND TO HEME IRON / Source: (gene. exp.) PHYSETER CATODON (sperm whale) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCO IS ATTACHED TO HEME IRON ATOM WHICH IS COORDINATED BY HIS 93A FROM THE MYOGLOBIN

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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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growpH: 9
Details: PROTEIN WAS CRYSTALLIZED FROM 3.6 M AMMONIUM SULFATE.CRYSTALS WERE SOAKED FOR C.A. 1 HOUR IN A THOROUGHLY DEGASSED AND CO SATURATED CRYOPROTECTANT SOLUTION MADE BY ADDITION OF 100 MG ...Details: PROTEIN WAS CRYSTALLIZED FROM 3.6 M AMMONIUM SULFATE.CRYSTALS WERE SOAKED FOR C.A. 1 HOUR IN A THOROUGHLY DEGASSED AND CO SATURATED CRYOPROTECTANT SOLUTION MADE BY ADDITION OF 100 MG XYLITOL, 100 MG GLUCOSE AND 8 MG NA-DITHIONATE TO 1 ML OF 70% SATURATED AMMONIUM SULFATE WITH 50 MM TRIS.HCL PH 9.0. DISTINCT COLOR CHANGES INDICATED THE FORMATION OF CO-MB FROM MET-MB.
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8.7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMprotein1drop
22.7 Mammonium sulfate1reservoir
320 mMTris-HCl1reservoir
41 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.91
DetectorType: PRINCETON SCIENTIFIC / Detector: CCD / Date: May 15, 1998 / Details: MIRRORS
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.4→19.6 Å / Num. obs: 40518 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.036 / Net I/σ(I): 19.8
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.125 / % possible all: 91.4
Reflection
*PLUS
Lowest resolution: 19.6 Å / Num. obs: 40518 / % possible obs: 96.5 % / Num. measured all: 143218 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 91.4 % / Num. unique obs: 7138 / Num. measured obs: 15373 / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 5.8

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→19.6 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.15312 -5 %
Rwork0.12845 --
obs-40518 96.5 %
Refinement stepCycle: LAST / Resolution: 1.4→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1231 0 60 258 1549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d2.545
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19.6 Å / Rfactor obs: 0.129 / Rfactor Rfree: 0.153 / Rfactor Rwork: 0.12845
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.014

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