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- PDB-3b0h: Assimilatory nitrite reductase (Nii4) from tobbaco root -

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Basic information

Entry
Database: PDB / ID: 3b0h
TitleAssimilatory nitrite reductase (Nii4) from tobbaco root
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: 2.306 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 9, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.d_res_high / _reflns_shell.d_res_low / _struct_ref_seq_dif.details
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_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_asym_id / _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_asym_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_asym_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_asym_id / _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_asym_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
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
B: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,19412
Polymers132,4372
Non-polymers2,75710
Water8,953497
1
A: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5976
Polymers66,2191
Non-polymers1,3785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5976
Polymers66,2191
Non-polymers1,3785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.343, 112.085, 92.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nitrite reductase / NII4


Mass: 66218.648 Da / Num. of mol.: 2 / Fragment: residues in UNP 19-584
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: nii4 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q76KA9, ferredoxin-nitrite reductase

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Non-polymers , 5 types, 507 molecules

#2: Chemical ChemComp-SRM / SIROHEME


Mass: 916.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: PEG4000, Tris-HCl, MgCl2, MPD, EDTA, PEG400, pH 8.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Nov 17, 2008 / Details: Rh-coated mirror
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 45883 / Num. obs: 45735 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.381.90.426198
2.38-2.4820.39198.2
2.48-2.5920.318198.9
2.59-2.7320.254199.2
2.73-2.920.206199.6
2.9-3.1220.154199.8
3.12-3.4420.109199.9
3.44-3.932.10.0721100
3.93-4.952.10.0511100
4.95-502.10.05199.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B0G

3b0g


Resolution: 2.306→46.25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.334 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.473 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 2315 5 %RANDOM
Rwork0.178 ---
obs0.1812 43569 100 %-
all-45883 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.8 Å2 / Biso mean: 25.8215 Å2 / Biso min: 4.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2---2.62 Å20 Å2
3---1.81 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.306→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8472 0 148 497 9117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228798
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.99411936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86151069
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9224.08402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.152151565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9711572
X-RAY DIFFRACTIONr_chiral_restr0.1040.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026590
X-RAY DIFFRACTIONr_nbd_refined0.2170.24316
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25956
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2530
X-RAY DIFFRACTIONr_metal_ion_refined0.2730.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.223
X-RAY DIFFRACTIONr_mcbond_it0.6241.55329
X-RAY DIFFRACTIONr_mcangle_it1.19328632
X-RAY DIFFRACTIONr_scbond_it1.96433497
X-RAY DIFFRACTIONr_scangle_it3.1754.53280
LS refinement shellResolution: 2.306→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 170 -
Rwork0.208 2899 -
all-3069 -
obs--100 %

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