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- PDB-1zj9: Structure of Mycobacterium tuberculosis NirA protein -

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Basic information

Entry
Database: PDB / ID: 1zj9
TitleStructure of Mycobacterium tuberculosis NirA protein
ComponentsProbable ferredoxin-dependent nitrite reductase NirA
KeywordsOXIDOREDUCTASE / NIRA / SULFITE / NITRITE / REDUCTASE / SIROHEME / FE4-S4 / CYS-TYR COVALENT BOND
Function / homology
Function and homology information


assimilatory sulfite reductase (ferredoxin) / Cysteine synthesis from O-acetylserine / sulfite reductase (ferredoxin) activity / sulfite reductase activity / sulfate assimilation / peptidoglycan-based cell wall / 4 iron, 4 sulfur cluster binding / heme binding / metal ion binding / cytosol
Similarity search - Function
Sulfite Reductase Hemoprotein;Domain 2 / 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 / 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 / Sulfite reductase [ferredoxin] / Sulfite reductase [ferredoxin]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSchnell, R. / Sandalova, T. / Hellman, U. / Lindqvist, Y. / Schneider, G.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Siroheme- and [Fe4-S4]-dependent NirA from Mycobacterium tuberculosis Is a Sulfite Reductase with a Covalent Cys-Tyr Bond in the Active Site
Authors: Schnell, R. / Sandalova, T. / Hellman, U. / Lindqvist, Y. / Schneider, G.
History
DepositionApr 28, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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 / struct_conn / struct_ncs_dom_lim / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: Probable ferredoxin-dependent nitrite reductase NirA
B: Probable ferredoxin-dependent nitrite reductase NirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,5798
Polymers126,9722
Non-polymers2,6086
Water28816
1
A: Probable ferredoxin-dependent nitrite reductase NirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7904
Polymers63,4861
Non-polymers1,3043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ferredoxin-dependent nitrite reductase NirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7904
Polymers63,4861
Non-polymers1,3043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.983, 83.307, 108.801
Angle α, β, γ (deg.)90.00, 102.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 10 - 555 / Label seq-ID: 21 - 566

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsthe biological assembly is a monomer in a complex with siroheme and FE4-S4 cluster

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Components

#1: Protein Probable ferredoxin-dependent nitrite reductase NirA / Sulfite reductase NirA


Mass: 63485.844 Da / Num. of mol.: 2 / Fragment: residues 3-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: NirA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P71753, UniProt: P9WJ03*PLUS, ferredoxin-nitrite reductase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-SRM / SIROHEME / Siroheme


Mass: 916.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.3 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, tris-HCl, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→60 Å / Num. all: 23209 / Num. obs: 23209 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 53.4 Å2 / Rsym value: 0.096 / Net I/σ(I): 5.6
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3413 / Rsym value: 0.338 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GET

2get


Resolution: 2.9→55 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.848 / SU B: 23.446 / SU ML: 0.433 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27998 1182 5.1 %RANDOM
Rwork0.20194 ---
all0.20605 22013 --
obs0.20605 22013 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.125 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-2.22 Å2
2---2.61 Å20 Å2
3---1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.9→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8632 0 144 16 8792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0218982
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.97512220
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69451090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29723.184446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.184151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1091596
X-RAY DIFFRACTIONr_chiral_restr0.0920.21294
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026976
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.24547
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.26028
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2332
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4951.55516
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84328668
X-RAY DIFFRACTIONr_scbond_it0.98134484
X-RAY DIFFRACTIONr_scangle_it1.594.53525
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4316 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.340.5
medium thermal0.652
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 92 -
Rwork0.293 1659 -
obs--99.83 %

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