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- PDB-1wvp: Structure of chemically modified myoglobin with distal N-tetrazol... -

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Basic information

Entry
Database: PDB / ID: 1wvp
TitleStructure of chemically modified myoglobin with distal N-tetrazolyl-histidine E7(64)
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / myoglobin / HEMOPROTEIN / Tetrazole / chemical modification / distal HisE7 / oxygen carrier / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / 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: 1.53 Å
AuthorsMakino, M. / Sugimoto, H. / Kamiya, N. / Shiro, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: J.Am.Chem.Soc. / Year: 1991
Title: Heme environmental structure of a novel artificial myoglobin with a closed heme pocket: site-specific chemical modification producing distal N-tetrazolylhistidine E7 by cyanogen bromide and azide ion
Authors: Kamiya, N. / Shiro, Y. / Iwata, T. / Iizuka, T. / Iwasaki, H.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Specific modification of structure and property of myoglobin by the formation of tetrazolylhistidine 64(E7). Reaction of the modified myoglobin with molecular oxygen
Authors: Shiro, Y. / Iwata, T. / Makino, R. / Fujii, M. / Isogai, Y. / Iizuka, T.
History
DepositionDec 23, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _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: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0954
Polymers17,2861
Non-polymers8093
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.982, 60.982, 84.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

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Components

#1: Protein Myoglobin /


Mass: 17285.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / Tissue: skeletal muscle / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.3 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 293 K / Method: batch / pH: 7
Details: Ammonium Sulfate, Phosphate, pH 7.0, batch, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 16, 2003
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. all: 24645 / Num. obs: 24611 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.94 Å2 / Rsym value: 0.05 / Net I/σ(I): 45.95
Reflection shellResolution: 1.53→1.58 Å / Mean I/σ(I) obs: 9.37 / Num. unique all: 2366 / Rsym value: 0.345 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A6K

1a6k


Resolution: 1.53→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.076 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1242 5.1 %RANDOM
Rwork0.174 ---
all0.175 23316 --
obs0.175 23316 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.043 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.53→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 53 159 1461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211341
X-RAY DIFFRACTIONr_angle_refined_deg1.5492.0561826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.025162
X-RAY DIFFRACTIONr_chiral_restr0.0960.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02999
X-RAY DIFFRACTIONr_nbd_refined0.260.2714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2112
X-RAY DIFFRACTIONr_metal_ion_refined0.0730.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.215
X-RAY DIFFRACTIONr_mcbond_it1.5131.5784
X-RAY DIFFRACTIONr_mcangle_it2.39621259
X-RAY DIFFRACTIONr_scbond_it3.2683557
X-RAY DIFFRACTIONr_scangle_it4.8984.5567
X-RAY DIFFRACTIONr_rigid_bond_restr1.64521341
X-RAY DIFFRACTIONr_sphericity_free3.8682159
X-RAY DIFFRACTIONr_sphericity_bonded3.57921302
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 82 -
Rwork0.162 1678 -
obs-2366 9.9 %

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