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- PDB-6r3y: M.tuberculosis nitrobindin with a cyanide molecule coordinated to... -

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Basic information

Entry
Database: PDB / ID: 6r3y
TitleM.tuberculosis nitrobindin with a cyanide molecule coordinated to the heme iron atom
ComponentsUPF0678 fatty acid-binding protein-like protein ERS007657_00996
KeywordsPROTEIN BINDING / hemeproteins / beta-barrel / peroxynitrite detoxification
Function / homology
Function and homology information


peroxynitrite isomerase activity / Isomerases; Other isomerases / heme binding / metal ion binding
Similarity search - Function
Nitrobindin, bacteria/plant / Nitrobindin family / THAP4-like, heme-binding beta-barrel domain / THAP4-like, heme-binding beta-barrel domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Peroxynitrite isomerase / Peroxynitrite isomerase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDe Simone, G. / di Masi, A. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. ...De Simone, G. / di Masi, A. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. / Tognaccini, L. / Smulevich, G. / Abbruzzetti, S. / Viappiani, C. / Bruno, S. / Ascenzi, P.
CitationJournal: Antioxid.Redox Signal. / Year: 2020
Title: Mycobacterial and Human Nitrobindins: Structure and Function.
Authors: De Simone, G. / di Masi, A. / Vita, G.M. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. / Tognaccini, L. / Smulevich, G. ...Authors: De Simone, G. / di Masi, A. / Vita, G.M. / Polticelli, F. / Pesce, A. / Nardini, M. / Bolognesi, M. / Ciaccio, C. / Coletta, M. / Turilli, E.S. / Fasano, M. / Tognaccini, L. / Smulevich, G. / Abbruzzetti, S. / Viappiani, C. / Bruno, S. / Ascenzi, P.
History
DepositionMar 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0678 fatty acid-binding protein-like protein ERS007657_00996
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5833
Polymers18,9401
Non-polymers6432
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-22 kcal/mol
Surface area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.818, 74.383, 80.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein UPF0678 fatty acid-binding protein-like protein ERS007657_00996


Mass: 18940.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Variant (production host): BL12 / References: UniProt: A0A0E8TXJ8, UniProt: P9WFG7*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.02 M NiCl2, 0.1 M Tris, PEG MM 2k 20%, 0.1 M potassium cyanide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→47 Å / Num. obs: 24489 / % possible obs: 100 % / Redundancy: 8 % / Net I/σ(I): 7.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3536 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fr2

2fr2


Resolution: 1.6→47 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.565 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20198 1164 4.8 %RANDOM
Rwork0.17802 ---
obs0.17913 23325 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.119 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.6→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 45 77 1346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131328
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171227
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.7071831
X-RAY DIFFRACTIONr_angle_other_deg1.2611.5992839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8825170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31621.11163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98615204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4861510
X-RAY DIFFRACTIONr_chiral_restr0.0630.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021514
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02284
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4751.134654
X-RAY DIFFRACTIONr_mcbond_other1.2311.126652
X-RAY DIFFRACTIONr_mcangle_it2.131.69817
X-RAY DIFFRACTIONr_mcangle_other2.1461.695818
X-RAY DIFFRACTIONr_scbond_it2.2761.376674
X-RAY DIFFRACTIONr_scbond_other2.2361.37672
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4631.9731009
X-RAY DIFFRACTIONr_long_range_B_refined4.66813.5261355
X-RAY DIFFRACTIONr_long_range_B_other4.65113.4391347
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 84 -
Rwork0.23 1703 -
obs--99.17 %

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