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- PDB-3b0l: M175G mutant of assimilatory nitrite reductase (Nii3) from tobbac... -

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Basic information

Entry
Database: PDB / ID: 3b0l
TitleM175G mutant of assimilatory nitrite reductase (Nii3) from tobbaco leaf
ComponentsNitrite reductase
KeywordsOXIDOREDUCTASE / siroheme / Fe4S4 binding protein
Function / homology
Function and homology information


ferredoxin-nitrite reductase / ferredoxin-nitrite reductase activity / nitrate assimilation / 4 iron, 4 sulfur cluster binding / heme binding / metal ion binding
Similarity search - Function
Sulfite Reductase Hemoprotein; domain 2 - #20 / : / Sulfite Reductase Hemoprotein; domain 2 / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain ...Sulfite Reductase Hemoprotein; domain 2 - #20 / : / Sulfite Reductase Hemoprotein; domain 2 / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / IRON/SULFUR CLUSTER / SIROHEME / Ferredoxin--nitrite reductase, chloroplastic
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNakano, S. / Takahashi, M. / Sakamoto, A. / Morikawa, H. / Katayanagi, K.
CitationJournal: Protein Sci. / Year: 2012
Title: Structure-function relationship of assimilatory nitrite reductases from the leaf and root of tobacco based on high resolution structures
Authors: Nakano, S. / Takahashi, M. / Sakamoto, A. / Morikawa, H. / Katayanagi, K.
History
DepositionJun 10, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 1, 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Dec 27, 2023Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8756
Polymers65,4971
Non-polymers1,3785
Water14,664814
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.271, 133.271, 77.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1114-

HOH

21A-1258-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitrite reductase / NII3


Mass: 65496.895 Da / Num. of mol.: 1 / Fragment: residues in UNP 19-580 / Mutation: M175G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Strain: K-12 / Gene: nii3 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q76KB0, ferredoxin-nitrite reductase

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Non-polymers , 5 types, 819 molecules

#2: Chemical ChemComp-SRM / SIROHEME


Mass: 916.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 814 / 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: 2.63 Å3/Da / Density % sol: 53.32 % / Mosaicity: 0.729 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: PEG4000, Tris-HCl, MgCl2, MPD, pH 8.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 25, 2009 / Details: Rh-coated Si single crystal mirror
RadiationMonochromator: Si(111) Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 74661 / Num. obs: 74661 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Χ2: 1.755 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.7-1.764.50.374.9473401.50296.2
1.76-1.834.60.2836.6573431.56996.2
1.83-1.914.80.2189.1473161.67495.7
1.91-2.025.10.15613.0873331.69195.7
2.02-2.145.40.11618.0972941.72295.1
2.14-2.315.60.09323.3972821.75894.6
2.31-2.545.80.07628.1273321.74395.2
2.54-2.915.80.05934.8475921.66397.7
2.91-3.6660.04248.6577321.75798.6
3.66-506.50.03861.4780972.20599.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B0G

3b0g


Resolution: 1.7→29.99 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.1947 / WRfactor Rwork: 0.1701 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8841 / SU B: 1.699 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0975 / SU Rfree: 0.0947 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 3757 5 %RANDOM
Rwork0.1765 ---
all0.1779 74579 --
obs0.1779 70822 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.81 Å2 / Biso mean: 18.96 Å2 / Biso min: 6.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refine analyzeLuzzati coordinate error obs: 0.171 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4243 0 74 814 5131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224415
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9955991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94924.167204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40315780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3561537
X-RAY DIFFRACTIONr_chiral_restr0.0920.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023323
X-RAY DIFFRACTIONr_nbd_refined0.2050.22263
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2601
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.266
X-RAY DIFFRACTIONr_mcbond_it0.61.52678
X-RAY DIFFRACTIONr_mcangle_it1.10624341
X-RAY DIFFRACTIONr_scbond_it1.99731748
X-RAY DIFFRACTIONr_scangle_it3.1534.51638
LS refinement shellResolution: 1.697→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 256 -
Rwork0.225 4961 -
obs--100 %

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