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- PDB-1abs: PHOTOLYSED CARBONMONOXY-MYOGLOBIN AT 20 K -

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Basic information

Entry
Database: PDB / ID: 1abs
TitlePHOTOLYSED CARBONMONOXY-MYOGLOBIN AT 20 K
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE / INTERMEDIATE IN LIGAND BINDING / 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 domain profile. / Globin-like / Globin / Globin / 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: 1.5 Å
AuthorsSchlichting, I. / Berendzen, J. / Phillips Jr., G.N. / Sweet, R.M.
Citation
Journal: Nature / Year: 1994
Title: Crystal structure of photolysed carbonmonoxy-myoglobin.
Authors: Schlichting, I. / Berendzen, J. / Phillips Jr., G.N. / Sweet, R.M.
#1: Journal: Proteins / Year: 1990
Title: Crystal Structure of Myoglobin from a Synthetic Gene
Authors: Phillips Jr., G.N. / Arduini, R.M. / Springer, B.A. / Sligar, S.G.
#2: 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 28, 1997Processing site: BNL
Revision 1.0Apr 1, 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)18,1064
Polymers17,3651
Non-polymers7413
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.420, 90.420, 45.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein MYOGLOBIN


Mass: 17365.164 Da / Num. of mol.: 1 / Mutation: D122N
Source method: isolated from a genetically manipulated source
Details: HEME BOUND TO HIS-93, PHOTOLYSED CO ATOP HEME / Source: (gene. exp.) Physeter catodon (sperm whale) / Description: SYNTHETIC GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / 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.: 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: 2

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.12 %
Description: DATA WERE COLLECTED UNDER CONTINUOUS ILLUMINATION USING AN OPEN FLOW HELIUM CRYOSTAT FOR COOLING.
Crystal growpH: 9
Details: PROTEIN WAS CRYSTALLIZED FROM 3.6 M AMMONIUM SULFATE. CRYSTALS WER SOAKED FOR 1 HOUR IN A THOROUGHLY DEGASSED AND N2 - SATURATED CRYOPROTECTANT SOLUTION MADE BY ADDITION OF 100 MG SUCROSE, ...Details: PROTEIN WAS CRYSTALLIZED FROM 3.6 M AMMONIUM SULFATE. CRYSTALS WER SOAKED FOR 1 HOUR IN A THOROUGHLY DEGASSED AND N2 - SATURATED CRYOPROTECTANT SOLUTION MADE BY ADDITION OF 100 MG SUCROSE, 100 MG GLUCOSE AND 8 MG NA-DITHIONATE TO 1 ML OF 70% SATURATED AMMONIUM SULFATE WITH 50 MM TRIS. HCL PH 9.0. THEN THE SOLUTION WAS EXCHANGED AGAINST A CO SATURATED ONE. DISTINCT COLOR CHANGES ACCOMPANIED THE FORMATION OF UNLIGATED MYOGLOBIN FROM MET-MB AND MBCO FROM UNLIGATED MB.
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
170 mg/mlprotein11
22.2-2.6 Mammonium sulfate11
320 mMTris-HCl11
41 mMEDTA11

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Data collection

DiffractionMean temperature: 20 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Mar 1, 1994 / Details: YES
RadiationMonochromator: YES / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionHighest resolution: 1.5 Å / Num. obs: 30947 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.063 / Rsym value: 0.068
Reflection shellResolution: 1.5→1.7 Å / % possible all: 78
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 93946 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 78 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
XSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 2MGK

2mgk


Resolution: 1.5→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / σ(F): 0
Details: HEME PARAMETERS WERE RELAXED TO ALLOW FOR REFINEMENT OF UNLIGATED, PHOTOLYSED, AND CO-BOUND COMPLEX.
RfactorNum. reflection% reflection
Rwork0.207 --
obs0.207 29798 89 %
Displacement parametersBiso mean: 6.4 Å2
Refine analyzeLuzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.06 Å
Refinement stepCycle: LAST / Resolution: 1.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 50 119 1394
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refine LS restraints NCSNCS model details: N.A
LS refinement shellResolution: 1.5→1.57 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.263 3348 -
obs--79.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROLSQ.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION4SO4.PARMSO4.TOP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor all: 0.263

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