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- PDB-1dws: PHOTOLYZED CARBONMONOXY MYOGLOBIN (HORSE HEART) -

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Basic information

Entry
Database: PDB / ID: 1dws
TitlePHOTOLYZED CARBONMONOXY MYOGLOBIN (HORSE HEART)
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / RESPIRATORY PROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / 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 speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsChu, K. / Vojtechovsky, J. / McMahon, B.H. / Sweet, R.M. / Berendzen, J. / Schlichting, I.
Citation
Journal: Nature / Year: 2000
Title: Crystal Structure of a New Ligand Binding Intermediate in Wildtype Carbonmonoxy Myoglobin
Authors: Chu, K. / Vojtechovsky, J. / Mcmahon, B.H. / Sweet, R.M. / Berendzen, J. / Schlichting, I.
#1: Journal: Biochim.Biophys.Acta / Year: 1997
Title: A Myoglobin Variant with a Polar Substitution in a Conserved Hydrophobic Cluster in the Heme Binding Pocket
Authors: Maurus, R. / Overall, C.M. / Bogumil, R. / Luo, Y. / Mauk, A.G. / Smith, M. / Brayer, G.D.
#2: Journal: Nature / Year: 1994
Title: Crystal Structure of Photolysed Myoglobin
Authors: Schlichting, I. / Berendzen, J. / Phillips Jr, G.N. / Sweet, R.M.
#3: Journal: J.Mol.Biol. / Year: 1987
Title: Crystallization and Preliminary Diffraction Data for Horse Heart Metmyoglobin
Authors: Sherwood, C. / Mauk, A.G. / Brayer, G.D.
History
DepositionDec 11, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: entity / entity_src_nat ...entity / entity_src_nat / pdbx_database_status / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_nat.common_name ..._entity.pdbx_description / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _pdbx_database_status.status_code_sf / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.5Dec 6, 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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8205
Polymers16,9841
Non-polymers8374
Water2,630146
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.300, 28.800, 35.500
Angle α, β, γ (deg.)90.00, 106.70, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

#1: Protein Myoglobin


Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: HEART / References: UniProt: P68082
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.82 Å3/Da / Density % sol: 32.6 %
Description: THIS DATASET WAS COLLECTED UNDER CONTINUOUS ILLUMIN USING A FIBER ILLUMINATOR AND AN OPEN STREAM HELIUM CRYOSTAT. PHOTOLYSIS OF THE BOUND CO WAS STARTED ONE PRIOR TO DATA COLLECTION.
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HHMB(SIGMA) WAS CRYSTALLIZED AT ROOM TEMPERATURE BY EQUILIBRATING 10 UL DROPS OF 5 MG/ML PROTEIN IN 1.7-1.8 M AMMONIUM SULFATE, 0.1 M TRIS HCL PH 7.5 USING THE HANGING DROP GEOMETRY
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
21.7-1.8 Mammonium sulfate1drop
30.1 MTris-HCl1drop
43.4-3.6 Mammonium sulfate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.91
DetectorType: BRANDEIS / Detector: CCD / Date: Jun 2, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 23278 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 7.3
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 1.48 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.195 / % possible all: 85.9
Reflection shell
*PLUS
% possible obs: 85.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AZI

1azi


Resolution: 1.45→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: LYS47 HAS ALTERNATE CONFORMATIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 -5 %RANDOM
Rwork0.204 ---
obs0.204 21223 95.9 %-
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 55 146 1395
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.93
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

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