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- PDB-1bzr: ATOMIC RESOLUTION CRYSTAL STRUCTURE ANALYSIS OF NATIVE DEOXY AND ... -

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Basic information

Entry
Database: PDB / ID: 1bzr
TitleATOMIC RESOLUTION CRYSTAL STRUCTURE ANALYSIS OF NATIVE DEOXY AND CO MYOGLOBIN FROM SPERM WHALE AT ROOM TEMPERATURE
ComponentsPROTEIN (MYOGLOBIN)
KeywordsOXYGEN STORAGE / CARBONMONOXY MYOGLOBIN / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsKachalova, G.S. / Popov, A.N. / 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 3, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MYOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0725
Polymers17,2351
Non-polymers8374
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.910, 31.040, 64.730
Angle α, β, γ (deg.)90.00, 105.53, 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.: 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.: 206 / 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: 1.96 Å3/Da / Density % sol: 37.25 %
Crystal growpH: 5.9
Details: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULPHATE, 0.1 M POTASSIUM PHOSPHATE, pH 5.9
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998 / 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: 1.15→20 Å / Num. obs: 46002 / % possible obs: 96.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 23.8
Reflection shellResolution: 1.15→1.2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.4 / % possible all: 95.3
Reflection
*PLUS
Num. measured all: 202454
Reflection shell
*PLUS
% possible obs: 95.3 %

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Processing

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

4mbn


Resolution: 1.15→12 Å / Num. parameters: 13701 / Num. restraintsaints: 17138 / 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
all0.124 46002 -
obs0.124 -96.3 %
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 40 / Occupancy sum hydrogen: 1156.6 / Occupancy sum non hydrogen: 1422.7
Refinement stepCycle: LAST / Resolution: 1.15→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 58 206 1567
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0.025
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.086
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.088
X-RAY DIFFRACTIONs_approx_iso_adps0.102
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.124
Solvent computation
*PLUS
Displacement parameters
*PLUS

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