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- PDB-1myz: CO COMPLEX OF MYOGLOBIN MB-YQR AT RT SOLVED FROM LAUE DATA. -

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Basic information

Entry
Database: PDB / ID: 1myz
TitleCO COMPLEX OF MYOGLOBIN MB-YQR AT RT SOLVED FROM LAUE DATA.
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN STORAGE / CO COMPLEX / RESPIRATORY PROTEIN / HEME / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid Body from starting model / Resolution: 1.6 Å
AuthorsBourgeois, D. / Vallone, B. / Schotte, F. / Arcovito, A. / Miele, A.E. / Sciara, G. / Wulff, M. / Anfinrud, P. / Brunori, M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography.
Authors: Bourgeois, D. / Vallone, B. / Schotte, F. / Arcovito, A. / Miele, A.E. / Sciara, G. / Wulff, M. / Anfinrud, P. / Brunori, M.
#1: Journal: Biophys.J. / Year: 1999
Title: Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10)
Authors: Brunori, M. / Cutruzzol, F. / Savino, C. / Travaglini-Allocatelli, C. / Vallone, B. / Gibson, Q.H.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin.
Authors: Brunori, M. / Vallone, B. / Cutruzzol, F. / Travaglini-Allocatelli, C. / Berendzen, J. / Chu, K. / Sweet, R.M. / Schlichting, I.
History
DepositionOct 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)18,2985
Polymers17,4611
Non-polymers8374
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.200, 91.200, 45.712
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-501-

SO4

21A-501-

SO4

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Components

#1: Protein Myoglobin


Mass: 17461.250 Da / Num. of mol.: 1 / Mutation: L29Y, H64Q, T67R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: pUC91 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1 / Keywords: L29(B10)Y, H64(E7)Q, T67(E10)R / 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.: 143 / 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: 10

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 294 K / pH: 8.7
Details: CO-saturated, 2.8M ammonium sulphate, 100mM Tris-Cl, 1 mM dithionite, crystallized in seeded batch, pH 8.7, temperature 294.0K
Crystal grow
*PLUS
pH: 9 / Method: batch method
Details: Phillips, G.N., (1990) Proteins Struct. Funct. Genet., 7, 358.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
170 mg/mlprotein11
22.2-2.6 Mammonium sulfate11
320 mMTris-HCl11

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 18, 2001
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.55→29.88 Å / Num. all: 31195 / Num. obs: 31195 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 26.7 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.064 / Net I/σ(I): 37.1
Reflection shellResolution: 1.55→1.62 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 3574 / Rsym value: 0.414 / % possible all: 75.9
Reflection
*PLUS
Num. measured all: 832442 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 75.9 % / Rmerge(I) obs: 0.414

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Processing

Software
NameVersionClassification
SPECdata collection
PROW+ CCP4data reduction
CNS1refinement
SPECdata reduction
PROWdata scaling
CCP4data scaling
CNS1phasing
RefinementMethod to determine structure: Rigid Body from starting model
Starting model: 1DXC (MbCO-YQR at 100K)

1dxc

100k


Resolution: 1.6→29.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1532735.67 / Data cutoff high rms absF: 1532735.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Sulfate 501 is on the 3 fold axis. Atoms S and O1 seat right on the axis and are given an occupancy of 0.33. Atoms O3 and O4 are generated by symmetry from atom O2. Unobserved (disordered) ...Details: Sulfate 501 is on the 3 fold axis. Atoms S and O1 seat right on the axis and are given an occupancy of 0.33. Atoms O3 and O4 are generated by symmetry from atom O2. Unobserved (disordered) atoms were removed from the ATOM list: 44 ASP OD2 62 LYS CE 62 LYS NZ 96 LYS CE 96 LYS NZ 98 LYS CD 98 LYS CE 98 LYS NZ 102 LYS CD 102 LYS CE 102 LYS NZ 140 LYS CD 140 LYS CE 140 LYS NZ 147 LYS CD 147 LYS CE 147 LYS NZ
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1422 5 %RANDOM
Rwork0.166 ---
all0.167 28574 --
obs0.167 28574 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 89.0488 Å2 / ksol: 0.359328 e/Å3
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.67 Å20 Å2
2--0.54 Å20 Å2
3----1.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1332 0 58 143 1533
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d15.9
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it3.412
X-RAY DIFFRACTIONc_scangle_it4.772.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 269 5.7 %
Rwork0.222 4456 -
obs-4456 98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1SUL.PARHEM_RELAX.TOP
X-RAY DIFFRACTION2CMO_PATCHED.PARCMO_PATCHED.TOP
X-RAY DIFFRACTION3HEM_RELAX.PARSUL.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0043
X-RAY DIFFRACTIONc_angle_deg1.03
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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