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- PDB-1zj8: Structure of Mycobacterium tuberculosis NirA protein -

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Basic information

Entry
Database: PDB / ID: 1zj8
TitleStructure of Mycobacterium tuberculosis NirA protein
ComponentsProbable ferredoxin-dependent nitrite reductase NirA
KeywordsOXIDOREDUCTASE / NIRA / SULFITE / NITRITE / REDUCTASE / SIROHEME / FE4-S4 / CYS-TYR COVALENT BOND / Structural Proteomics in Europe / SPINE / Structural Genomics
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 ...: / 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 / 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 / Sulfite reductase [ferredoxin] / Sulfite reductase [ferredoxin]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSchnell, R. / Sandalova, T. / Hellman, U. / Lindqvist, Y. / Schneider, G. / Structural Proteomics in Europe (SPINE)
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 1.3May 23, 2018Group: Data collection / Category: diffrn_source / struct_biol / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 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
Revision 2.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water39622
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)84.257, 115.355, 114.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: 2 / Auth seq-ID: 10 - 555 / Label seq-ID: 21 - 566

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsTHE BIOLOGICAL ASSEMBLY IS A MONOMER.

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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


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


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


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


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 45.7 %
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: MAX II / Beamline: I711 / Wavelength: 1.085 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.085 Å / Relative weight: 1
ReflectionResolution: 2.8→45 Å / Num. obs: 28218 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 55.37 Å2 / Rsym value: 0.109 / Net I/σ(I): 17.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 4049 / Rsym value: 0.469 / % possible all: 100

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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: 2GEP

2gep


Resolution: 2.8→30.65 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.853 / SU B: 18.396 / SU ML: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29203 1436 5.1 %RANDOM
Rwork0.21469 ---
all0.21866 25727 --
obs0.21866 26720 100 %-
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: 43.728 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20 Å2
2---1.27 Å20 Å2
3---2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8632 0 144 22 8798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0218995
X-RAY DIFFRACTIONr_bond_other_d0.0020.028162
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.97512220
X-RAY DIFFRACTIONr_angle_other_deg0.873318870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50451090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46223.184446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.909151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4651596
X-RAY DIFFRACTIONr_chiral_restr0.0770.21294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210096
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021884
X-RAY DIFFRACTIONr_nbd_refined0.2180.21936
X-RAY DIFFRACTIONr_nbd_other0.1880.28909
X-RAY DIFFRACTIONr_nbtor_refined0.1750.24311
X-RAY DIFFRACTIONr_nbtor_other0.0860.25419
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0790.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7751.56946
X-RAY DIFFRACTIONr_mcbond_other0.1021.52242
X-RAY DIFFRACTIONr_mcangle_it0.86428668
X-RAY DIFFRACTIONr_scbond_it0.92434763
X-RAY DIFFRACTIONr_scangle_it1.4744.53523
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 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
3198tight positional0.040.05
5165medium positional0.260.5
3198tight thermal0.090.5
5165medium thermal0.392
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 96 -
Rwork0.311 1933 -
obs--100 %

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