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- PDB-3v2v: Nitrite Bound Chlorin Substituted Myoglobin- Method 1 -

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Basic information

Entry
Database: PDB / ID: 3v2v
TitleNitrite Bound Chlorin Substituted Myoglobin- Method 1
ComponentsMyoglobin
KeywordsTRANSPORT PROTEIN / nitrite / chlorin / myoglobin / chlorin reconstituted myoglobin
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
Fe(III) pyropheophorbide-a methyl ester / NITRITE ION / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsYi, J. / Thomas, L.M. / Ricther-Addo, G.B.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Distal pocket control of nitrite binding in myoglobin
Authors: Yi, J. / Thomas, L.M. / Richter-Addo, G.B.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_validate_chiral / 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.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_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)17,9398
Polymers16,9841
Non-polymers9567
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.432, 30.519, 63.579
Angle α, β, γ (deg.)90.00, 105.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin


Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Tissue: heart / References: UniProt: P68082

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Non-polymers , 5 types, 157 molecules

#2: Chemical ChemComp-HKL / Fe(III) pyropheophorbide-a methyl ester


Mass: 602.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O3
#3: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium sulfate, 100mM TrisHCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 21, 2010 / Details: Osmic
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→26.45 Å / Num. obs: 15443 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.13 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 17.8
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.08 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1503 / % possible all: 95.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BA2

3ba2


Resolution: 1.65→26.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.298 / SU ML: 0.078 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.128 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 787 5.1 %RANDOM
Rwork0.19177 ---
obs0.1932 14594 98.32 %-
all-15443 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.747 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å20.19 Å2
2---0.4 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.65→26.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 62 150 1406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211286
X-RAY DIFFRACTIONr_angle_refined_deg2.0172.0131740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7985151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36125.09453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40115229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.978152
X-RAY DIFFRACTIONr_chiral_restr0.1290.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021946
X-RAY DIFFRACTIONr_mcbond_it1.3021.5755
X-RAY DIFFRACTIONr_mcangle_it2.26721191
X-RAY DIFFRACTIONr_scbond_it3.4043531
X-RAY DIFFRACTIONr_scangle_it5.1394.5549
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.517 49 -
Rwork0.459 1026 -
obs--94.3 %

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