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- PDB-1a6m: OXY-MYOGLOBIN, ATOMIC RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1a6m
TitleOXY-MYOGLOBIN, ATOMIC RESOLUTION
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / HEME PROTEIN / MODEL COMPOUNDS / OXYGEN STORAGE / LIGAND BINDING GEOMETRY / CONFORMATIONAL SUBSTATES
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
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsVojtechovsky, J. / Chu, K. / Berendzen, J. / Sweet, R.M. / Schlichting, I.
CitationJournal: Biophys.J. / Year: 1999
Title: Crystal structures of myoglobin-ligand complexes at near-atomic resolution.
Authors: Vojtechovsky, J. / Chu, K. / Berendzen, J. / Sweet, R.M. / Schlichting, I.
History
DepositionFeb 26, 1998Processing site: BNL
Revision 1.0Apr 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / 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 / _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)17,8905
Polymers17,0501
Non-polymers8414
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.800, 30.810, 34.350
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYOGLOBIN


Mass: 17049.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.9 Å3/Da / Density % sol: 36 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
250 mg/mlmyoglobin11
350 mMpotassium phosphate11
1ammonium sulfate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.84
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 67676 / % possible obs: 97 % / Observed criterion σ(I): -3 / Rsym value: 0.057 / Net I/σ(I): 26
Reflection shellResolution: 1→1.1 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.232 / % possible all: 88
Reflection
*PLUS
Num. measured all: 530931 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 88 % / Rmerge(I) obs: 0.232

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MBC

1mbc


Resolution: 1→8 Å / Num. parameters: 14251 / Num. restraintsaints: 18357 / Cross valid method: FREE R-VALUE
StereochEM target val spec case: HEME - PARAMETERS BASED ON CSD
Stereochemistry target values: ENGH & HUBER
Details: NO GEOMETRIC RESTRAINTS APPLIED TO IRON AND THE PLANAR ATOMS OF THE HEME. BAYESIAN WEIGHTING WAS APPLIED TO THE REFLECTION SET AT THE FINAL ROUND OF REFINEMENT. SEE TERWILLIGER AND ...Details: NO GEOMETRIC RESTRAINTS APPLIED TO IRON AND THE PLANAR ATOMS OF THE HEME. BAYESIAN WEIGHTING WAS APPLIED TO THE REFLECTION SET AT THE FINAL ROUND OF REFINEMENT. SEE TERWILLIGER AND BERENDZEN, ACTA CRYST. D52:743-748 (1996). THE SOLVENT MOLECULES 129 AND 139 CAN BE MODELED ONLY FOR ONE ALTERNATIVE PROTEIN CONFORMATION.
RfactorNum. reflection% reflection
Rfree0.1587 3300 5 %
all0.1269 65436 -
obs0.122 -94 %
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 26 / Occupancy sum hydrogen: 1263 / Occupancy sum non hydrogen: 1426.8
Refinement stepCycle: LAST / Resolution: 1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 55 186 1577
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.023
X-RAY DIFFRACTIONs_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.121
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.075

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