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- PDB-3vlx: Assimilatory nitrite reductase (Nii3) - N226K mutant - ligand fre... -

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Basic information

Entry
Database: PDB / ID: 3vlx
TitleAssimilatory nitrite reductase (Nii3) - N226K mutant - ligand free form from tobacco leaf
ComponentsNitrite reductase
KeywordsOXIDOREDUCTASE / Nii3 N226K mutant / ligand free / 3 alpha/beta domains / reductase
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 / molecular replacement / Resolution: 1.35 Å
AuthorsNakano, S. / Takahashi, M. / Sakamoto, A. / Morikawa, H. / Katayanagi, K.
CitationJournal: Chem.Biodivers. / Year: 2012
Title: X-ray crystal structure of a mutant assimilatory nitrite reductase that shows sulfite reductase-like activity
Authors: Nakano, S. / Takahashi, M. / Sakamoto, A. / Morikawa, H. / Katayanagi, K.
History
DepositionDec 5, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 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_struct_conn_angle / pdbx_struct_special_symmetry / 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)67,0007
Polymers65,5861
Non-polymers1,4146
Water16,538918
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.498, 133.498, 77.770
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

31A-1464-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitrite reductase


Mass: 65586.125 Da / Num. of mol.: 1 / Fragment: UNP residues 19-580 / Mutation: N226K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / 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, 924 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.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 918 / 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: 53.44 % / Mosaicity: 0.22 °
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: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 7, 2010 / Details: Rh coated collimating and focusing Si 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: 1.35→50 Å / Num. all: 152951 / Num. obs: 152951 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.051 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.35-1.413.80.4684.68150840.599100
1.4-1.45140.3786.39151540.615100
1.45-1.5214.10.2848.67151230.644100
1.52-1.614.30.21312.17151670.693100
1.6-1.714.40.16416.89151990.744100
1.7-1.8314.50.12423.53152150.816100
1.83-2.0214.60.09234.83152700.964100
2.02-2.3114.80.07248.55153381.165100
2.31-2.9114.80.05961.68154611.359100
2.91-5014.20.05884.08159402.78199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B0G

3b0g


Resolution: 1.35→47.19 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1646 / WRfactor Rwork: 0.1555 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.913 / SU B: 0.567 / SU ML: 0.024 / SU R Cruickshank DPI: 0.0464 / SU Rfree: 0.0457 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1748 7671 5 %RANDOM
Rwork0.1644 ---
all0.1649 152899 --
obs0.1649 152899 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: 146.15 Å2 / Biso mean: 14.7481 Å2 / Biso min: 5.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.126 Å
Refinement stepCycle: LAST / Resolution: 1.35→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 75 918 5241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224421
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9955997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25924.167204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76315787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3541537
X-RAY DIFFRACTIONr_chiral_restr0.0830.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023323
X-RAY DIFFRACTIONr_nbd_refined0.1990.22235
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2729
X-RAY DIFFRACTIONr_metal_ion_refined0.1820.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.286
X-RAY DIFFRACTIONr_mcbond_it0.4631.52679
X-RAY DIFFRACTIONr_mcangle_it0.92624344
X-RAY DIFFRACTIONr_scbond_it1.53631753
X-RAY DIFFRACTIONr_scangle_it2.5074.51641
LS refinement shellResolution: 1.351→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 562 -
Rwork0.229 10521 -
all-11083 -
obs--100 %

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