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- PDB-8j4w: Structure of Mycobacterium thermoresistibile NrdI(reduced) determ... -

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Basic information

Entry
Database: PDB / ID: 8j4w
TitleStructure of Mycobacterium thermoresistibile NrdI(reduced) determined at 1.1 angstrom resolution
ComponentsProtein NrdI
KeywordsFLAVOPROTEIN / Ribonucleotide reductase accessory protein. Metal cofactor assembly
Function / homology
Function and homology information


protein modification process / FMN binding
Similarity search - Function
Ribonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / HYDROGEN PEROXIDE / PEROXIDE ION / SULFITE ION / Protein NrdI
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsYadav, L.R. / Mande, S.C.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)DST-NPDF (PDF/2015/000961) and DBT-Centre of Excellence Grant (BT/PR15450/COE/34/46/2016). India
CitationJournal: Curr Res Struct Biol / Year: 2024
Title: Structural insights into the initiation of free radical formation in the Class Ib ribonucleotide reductases in Mycobacteria.
Authors: Yadav, L.R. / Sharma, V. / Shanmugam, M. / Mande, S.C.
History
DepositionApr 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0806
Polymers16,4431
Non-polymers6385
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Monomer prottein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-7 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.737, 36.840, 48.371
Angle α, β, γ (deg.)90.000, 111.530, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules C

#1: Protein Protein NrdI


Mass: 16442.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ribonucleotide reductase cofactor assembly protein
Source: (gene. exp.) Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Strain: ATCC 19527 / Gene: nrdI / Plasmid: pET32a+ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 (DE3) / References: UniProt: G7CEK1

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Non-polymers , 6 types, 164 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#5: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 1.8 Å3/Da / Density % sol: 31.72 % / Description: Rectangular crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.15M potassium phosphate monobasic and 18% PEG 3350. For reduction crystals are soaked in sodium dithionite solution
PH range: 7.5-8.2 / Temp details: 293.15

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2017
RadiationMonochromator: a single-bounce silicon (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→45 Å / Num. obs: 3774695 / % possible obs: 99.87 % / Redundancy: 106.1 % / Biso Wilson estimate: 9.2 Å2 / CC1/2: 0.96 / CC star: 0.99 / Net I/σ(I): 50.08
Reflection shellResolution: 1.214→1.257 Å / Redundancy: 104.6 % / Num. unique obs: 3510 / CC1/2: 0.86 / CC star: 0.96 / % possible all: 99.24

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→45 Å / SU ML: 0.0952 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.9585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.171 1788 5.03 %
Rwork0.1372 33731 -
obs0.1389 3774695 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15 Å2
Refinement stepCycle: LAST / Resolution: 1.21→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 40 159 1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521228
X-RAY DIFFRACTIONf_angle_d0.92691683
X-RAY DIFFRACTIONf_chiral_restr0.0789181
X-RAY DIFFRACTIONf_plane_restr0.0084216
X-RAY DIFFRACTIONf_dihedral_angle_d20.9115448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.250.20141140.17262583X-RAY DIFFRACTION99.08
1.25-1.280.22371460.17132564X-RAY DIFFRACTION99.78
1.28-1.320.23191400.16062577X-RAY DIFFRACTION99.82
1.32-1.370.19041280.14812586X-RAY DIFFRACTION99.96
1.37-1.430.17871230.14292604X-RAY DIFFRACTION99.96
1.43-1.490.15251470.13012566X-RAY DIFFRACTION99.96
1.49-1.570.15831290.11762589X-RAY DIFFRACTION99.93
1.57-1.670.15711520.11452591X-RAY DIFFRACTION100
1.67-1.80.15211240.11982612X-RAY DIFFRACTION100
1.8-1.980.13981390.12482576X-RAY DIFFRACTION99.96
1.98-2.270.17161380.12842614X-RAY DIFFRACTION100
2.27-2.850.15251430.14862613X-RAY DIFFRACTION99.96
2.85-450.18481650.14022656X-RAY DIFFRACTION99.96

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