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- PDB-3b0n: Q448K mutant of assimilatory nitrite reductase (Nii3) from tobbac... -

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Basic information

Entry
Database: PDB / ID: 3b0n
TitleQ448K 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 / 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 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily ...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 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / IRON/SULFUR CLUSTER / SIROHEME / Nitrite reductase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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

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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)66,9506
Polymers65,5721
Non-polymers1,3785
Water11,007611
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.455, 133.455, 77.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1240-

HOH

21A-1383-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitrite reductase / / NII3


Mass: 65572.094 Da / Num. of mol.: 1 / Fragment: residues in UNP 19-580 / Mutation: Q448K
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, 616 molecules

#2: Chemical ChemComp-SRM / SIROHEME / Siroheme


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


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


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.64 Å3/Da / Density % sol: 53.35 % / Mosaicity: 0.665 °
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: Feb 24, 2010 / 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: 2→50 Å / Num. all: 47946 / Num. obs: 47946 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Χ2: 1.707 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2-2.07130.4168.0946851.42199.6
2.07-2.15130.33710.3447251.44899.7
2.15-2.2513.10.26413.347061.49599.8
2.25-2.3713.10.21417.0447451.55100
2.37-2.5213.20.16821.1847621.562100
2.52-2.7113.20.13227.6847731.599100
2.71-2.9913.30.10236.2147771.61799.9
2.99-3.4213.70.07253.0948181.71499.9
3.42-4.3114.20.05573.2348831.97100
4.31-5013.60.05479.5750722.55799.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.66 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1752 / WRfactor Rwork: 0.1447 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8982 / SU B: 2.77 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1373 / SU Rfree: 0.1245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 2426 5.1 %RANDOM
Rwork0.1541 ---
all0.1557 47910 --
obs0.1557 45484 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: 97.6 Å2 / Biso mean: 26.1438 Å2 / Biso min: 10.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.41 Å2
Refine analyzeLuzzati coordinate error obs: 0.177 Å
Refinement stepCycle: LAST / Resolution: 2→30.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 74 611 4932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224419
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9965995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23924.138203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59315785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3251537
X-RAY DIFFRACTIONr_chiral_restr0.0980.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023319
X-RAY DIFFRACTIONr_nbd_refined0.210.22152
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2493
X-RAY DIFFRACTIONr_metal_ion_refined0.2270.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2970.256
X-RAY DIFFRACTIONr_mcbond_it0.731.52679
X-RAY DIFFRACTIONr_mcangle_it1.37824344
X-RAY DIFFRACTIONr_scbond_it2.40831751
X-RAY DIFFRACTIONr_scangle_it3.9364.51639
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 193 -
Rwork0.174 3250 -
obs--100 %

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