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- PDB-1ajg: CARBONMONOXY MYOGLOBIN AT 40 K -

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Basic information

Entry
Database: PDB / ID: 1ajg
TitleCARBONMONOXY MYOGLOBIN AT 40 K
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / RESPIRATORY PROTEIN / HEME
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 / DIFFERENCE FOURIER / Resolution: 1.69 Å
AuthorsTeng, T.Y. / Srajer, V. / Moffat, K.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: Photolysis-induced structural changes in single crystals of carbonmonoxy myoglobin at 40 K.
Authors: Teng, T.Y. / Srajer, V. / Moffat, K.
#1: Journal: Biochemistry / Year: 1997
Title: Initial Trajectory of Carbon Monoxide After Photodissociation from Myoglobin at Cryogenic Temperatures
Authors: Teng, T.Y. / Srajer, V. / Moffat, K.
History
DepositionMay 2, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)18,0725
Polymers17,2351
Non-polymers8374
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.430, 30.430, 34.120
Angle α, β, γ (deg.)90.00, 105.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYOGLOBIN


Mass: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CARBONMONOXY MYOGLOBIN, CO LIGAND BOUND TO FE OF THE HEME, HEME BOUND TO NE2 OF HIS 93
Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185
#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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.84 Å3/Da / Density % sol: 33.12 %
Description: DATA WERE COLLECTED IN DARK USING AN OPEN FLOW NITROGEN/HELIUM CRYOSTAT FOR COOLING.
Crystal growpH: 6
Details: AS DESCRIBED IN KENDREW,J.C. AND PARRISH,R.G., PROC. ROY. SOC. A (LONDON) 238, 305-324 (1956), pH 6.0
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 40 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.123
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 30, 1993 / Details: YES
RadiationMonochromator: YES / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.123 Å / Relative weight: 1
ReflectionResolution: 1.69→27.5 Å / Num. obs: 13483 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 10.7
Reflection shellResolution: 1.69→1.77 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 5.1 / % possible all: 83.5

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1MBO

1mbo


Resolution: 1.69→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
Details: THE FOLLOWING RESIDUES HAVE BEEN MODELED WITH DISORDERED SIDE CHAINS IN TWO CONFORMERS -- 4 GLU, 21 VAL, 26 GLN, 31 ARG, 61 LEU. IN ADDITION, THE LIGAND CARBONMONOXY WAS REFINED IN SUCH WAY ...Details: THE FOLLOWING RESIDUES HAVE BEEN MODELED WITH DISORDERED SIDE CHAINS IN TWO CONFORMERS -- 4 GLU, 21 VAL, 26 GLN, 31 ARG, 61 LEU. IN ADDITION, THE LIGAND CARBONMONOXY WAS REFINED IN SUCH WAY OF SHARING ELECTRON DENSITY WITH 30% WATER MOLECULE TO SIMULATE THE 30% MET MYOGLOBIN CONTENTS IN THE VERY LAST STAGE OF REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1364 10 %RANDOM
Rwork0.171 ---
obs0.171 13385 94.5 %-
Refine analyzeLuzzati coordinate error obs: 0.16 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.08 Å
Refinement stepCycle: LAST / Resolution: 1.69→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 45 193 1455
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.69→1.77 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.29 136 10 %
Rwork0.227 1302 -
obs--82.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHSCDX.PRO
X-RAY DIFFRACTION2PARHCSDX.HEMETOPHSCDX.HEME
X-RAY DIFFRACTION3PARAM19X.COTOPH19X.CO
X-RAY DIFFRACTION4PARAM19X.H2OTOPH19X.H20
Refinement
*PLUS
Rfactor obs: 0.171 / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.29 / Rfactor Rwork: 0.227

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