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- PDB-1bz6: ATOMIC RESOLUTION CRYSTAL STRUCTURE AQUOMET-MYOGLOBIN FROM SPERM ... -

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Basic information

Entry
Database: PDB / ID: 1bz6
TitleATOMIC RESOLUTION CRYSTAL STRUCTURE AQUOMET-MYOGLOBIN FROM SPERM WHALE AT ROOM TEMPERATURE
ComponentsPROTEIN (MYOGLOBIN)
KeywordsOXYGEN STORAGE / OXYGEN TRANSPORT / RESPIRATORY PROTEIN / HEME / ATOMIC RESOLUTION
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: 1.2 Å
AuthorsPopov, A.N. / Kachalova, G.S. / Bartunik, H.D.
CitationJournal: Science / Year: 1999
Title: A steric mechanism for inhibition of CO binding to heme proteins.
Authors: Kachalova, G.S. / Popov, A.N. / Bartunik, H.D.
History
DepositionNov 5, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (MYOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2366
Polymers17,2351
Non-polymers1,0015
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.830, 30.920, 64.570
Angle α, β, γ (deg.)90.00, 105.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (MYOGLOBIN)


Mass: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / Tissue: MUSCLE / References: UniProt: P02185
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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.: 223 / 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: 1.94 Å3/Da / Density % sol: 36.71 %
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULPHATE, 0.1 M POTASSIUM PHOSPHATE, pH 6.0
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→60 Å / Num. obs: 41547 / % possible obs: 99.4 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 30.4
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 6.6 / % possible all: 100
Reflection
*PLUS
Num. measured all: 564343
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MBN

4mbn


Resolution: 1.2→12 Å / Num. parameters: 14814 / Num. restraintsaints: 20313 / σ(F): 0
StereochEM target val spec case: HEME - PARAMETERS BASED ON CSD
Stereochemistry target values: ENGH AND HUBER
Details: NO GEOMETRIC RESTRAINTS APPLIED TO IRON ATOM AND HEME PLANARITY
RfactorNum. reflection% reflection
obs0.091 -99.4 %
all-41485 -
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 81 / Occupancy sum hydrogen: 1034.6 / Occupancy sum non hydrogen: 1436.8
Refinement stepCycle: LAST / Resolution: 1.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 68 223 1691
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0.014
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.107
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.012
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.104
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.112
Solvent computation
*PLUS
Displacement parameters
*PLUS

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