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- PDB-1a6k: AQUOMET-MYOGLOBIN, ATOMIC RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1a6k
TitleAQUOMET-MYOGLOBIN, ATOMIC RESOLUTION
ComponentsMYOGLOBIN
KeywordsHEME 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-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 speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsVojtechovsky, J. / Berendzen, J. / Chu, K. / Schlichting, I. / Sweet, R.M.
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 24, 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)17,9545
Polymers17,0501
Non-polymers9054
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.900, 30.730, 34.360
Angle α, β, γ (deg.)90.00, 105.70, 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.: 3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jan 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 51794 / % possible obs: 98 % / Observed criterion σ(I): -3 / Rsym value: 0.046 / Net I/σ(I): 25
Reflection shellResolution: 1.1→1.15 Å / Mean I/σ(I) obs: 6 / Rsym value: 0.295 / % possible all: 97
Reflection
*PLUS
Num. measured all: 302654 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.295

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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: 1.1→8 Å / Num. parameters: 14244 / Num. restraintsaints: 18493 / 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 DIFFERENCE REFINEMENT WAS USED AT THE FINAL STEP. SEE TERWILLIGER AND BERENDZEN, ACTA CRYST. D52:1004-1011. ...Details: NO GEOMETRIC RESTRAINTS APPLIED TO IRON AND THE PLANAR ATOMS OF THE HEME. BAYESIAN DIFFERENCE REFINEMENT WAS USED AT THE FINAL STEP. SEE TERWILLIGER AND BERENDZEN, ACTA CRYST. D52:1004-1011. (1996). THE SOLVENT MOLECULES 81, 129, 130, 139 AND 151 CAN BE MODELED ONLY FOR ONE ALTERNATIVE PROTEIN CONFORMATION. SULFATE NEAR DISTAL HISTIDINE MODELED AS A DISORDERED MOLECULE.
RfactorNum. reflection% reflection
Rfree0.1525 2541 5 %
all0.1323 51286 -
obs0.1312 -98 %
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 26 / Occupancy sum hydrogen: 1263 / Occupancy sum non hydrogen: 1420
Refinement stepCycle: LAST / Resolution: 1.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1324 0 53 185 1562
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.023
X-RAY DIFFRACTIONs_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.127
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0.071

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