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- PDB-1h1x: Sperm whale Myoglobin mutant T67R S92D -

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Basic information

Entry
Database: PDB / ID: 1h1x
TitleSperm whale Myoglobin mutant T67R S92D
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / GLOBIN / PEROXIDASE / OXYGEN STORAGE / HEME / MUSCLE
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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPHYSETER CATODON (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZuccotti, S. / Bolognesi, M.
Citation
Journal: Biochem.J. / Year: 2004
Title: Engineering Peroxidase Activity in Myoglobin: The Haem Cavity Structure and Peroxide Activation in the T67R/S92D Mutant and its Derivative Reconstituted with Protohaemin-L-Histidine.
Authors: Roncone, R. / Monzani, E. / Murtas, M. / Battaini, G. / Pennati, A. / Sanangelantoni, A.M. / Zuccotti, S. / Bolognesi, M. / Casella, L.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: High-Resolution Crystal Structures of Distal Histidine Mutants of Sperm Whale Myoglobin
Authors: Quillin, M.L. / Arduini, R.M. / Olson, J.S. / Phillips Jr, G.N.
History
DepositionJul 25, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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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)18,1884
Polymers17,4491
Non-polymers7393
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.524, 90.524, 45.129
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein MYOGLOBIN


Mass: 17449.262 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: MUTATION THR 67 ARG AND SER 92 ASP / Source: (gene. exp.) PHYSETER CATODON (sperm whale) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02185
#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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMEMBER OF THE GLOBIN FAMILY SERVING AS RESERVIOR OF OXYGEN IN MUSCLE CELLS ENGINEERED MUTATION THR ...MEMBER OF THE GLOBIN FAMILY SERVING AS RESERVIOR OF OXYGEN IN MUSCLE CELLS ENGINEERED MUTATION THR 67 ARG AND SER 92 ASP
Sequence detailsREFERENCE BIOCHIM. BIOPHYS. ACTA 336:318-323(1974) SHOWS CONFLICT AT POSITION 122 OF THE PROTEIN ...REFERENCE BIOCHIM. BIOPHYS. ACTA 336:318-323(1974) SHOWS CONFLICT AT POSITION 122 OF THE PROTEIN SEQUENCE AS INDICATED IN THE DBREF RECORDS BELOW.

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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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growpH: 9
Details: 3M (NH4)2SO4, 5MM K3FE(CN)6, 20MM TRIS/HCL, PH9.0, DROPLET 5:3, RESERVOIR:PROTEIN (43MG/ML), pH 9.00
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.05 Mphosphate1droppH6.0
243 mg/mlprotein1drop
33.0 Mammonium sulfate1reservoir
40.005 M1reservoirK3Fe(CN)6
50.005 M1reservoirKCN
60.20 MTris-HCl1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorDetector: CCD / Date: Apr 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→19 Å / Num. obs: 41560 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 13.51 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 28.97
Reflection shellResolution: 1.4→1.44 Å / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 3.84
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 19 Å / Redundancy: 13.51 % / Num. measured all: 561360 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 3.84

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FCS

1fcs


Resolution: 1.4→19 Å / SU B: 1.47 / SU ML: 0.024 / ESU R: 0.044 / ESU R Free: 0.044
Details: C-TERMINAL RESIDUES (Q152, G153) LIE IN A POORLY DEFINED ELECTRON DENSITY REGION.
RfactorNum. reflection% reflectionSelection details
Rfree0.153 2069 5 %RANDOM
Rwork0.119 ---
obs0.121 41560 99.1 %-
Displacement parametersBiso mean: 16.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1231 0 50 302 1583
Refinement
*PLUS
Rfactor Rfree: 0.15 / Rfactor Rwork: 0.12
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.015
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.57
X-RAY DIFFRACTIONplane_restr0.016

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