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- PDB-8j4v: Structure of Mycobacterium thermoresistibile NrdI(oxidised) deter... -

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Basic information

Entry
Database: PDB / ID: 8j4v
TitleStructure of Mycobacterium thermoresistibile NrdI(oxidised) determined at 1.1 angstrom resolution
ComponentsProtein NrdI
KeywordsFLAVOPROTEIN / Ribonucleotide reductase accessory protein. Metal cofactor assembly
Function / homologyRibonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / Flavoprotein-like superfamily / protein modification process / FMN binding / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Protein NrdI
Function and homology information
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 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)17,0864
Polymers16,4431
Non-polymers6433
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-7 kcal/mol
Surface area8450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.010, 37.200, 48.380
Angle α, β, γ (deg.)90.000, 111.610, 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

#1: Protein Protein NrdI


Mass: 16442.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ribonucleotide reductase Metal cofactor
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
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
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: 1.83 Å3/Da / Density % sol: 32.87 %
Description: Rectangular yellow color small sized crystals of 50-80 micron
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.15M potassium phosphate monobasic and 18% PEG 3350
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: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.11→44.98 Å / Num. obs: 47159 / % possible obs: 99.77 % / Redundancy: 12.6 % / Biso Wilson estimate: 7.59 Å2 / CC1/2: 0.793 / CC star: 0.94 / Net I/σ(I): 35.82
Reflection shellResolution: 1.11→1.15 Å / Redundancy: 11.2 % / Num. unique obs: 4696 / CC1/2: 0.628 / CC star: 0.878 / % possible all: 99.68

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.11→44.98 Å / SU ML: 0.0884 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.1213
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1579 2317 4.92 %
Rwork0.1379 44748 -
obs0.139 47065 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.49 Å2
Refinement stepCycle: LAST / Resolution: 1.11→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1122 0 42 127 1291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461303
X-RAY DIFFRACTIONf_angle_d0.89971803
X-RAY DIFFRACTIONf_chiral_restr0.0815196
X-RAY DIFFRACTIONf_plane_restr0.006234
X-RAY DIFFRACTIONf_dihedral_angle_d5.5164201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.130.2141410.18332609X-RAY DIFFRACTION99.64
1.13-1.160.18731550.15342614X-RAY DIFFRACTION99.71
1.16-1.180.19561090.14042613X-RAY DIFFRACTION99.89
1.18-1.210.14821340.13752619X-RAY DIFFRACTION99.39
1.21-1.250.15411470.12742633X-RAY DIFFRACTION99.89
1.25-1.280.14091120.13272649X-RAY DIFFRACTION100
1.28-1.320.1561180.12442635X-RAY DIFFRACTION99.96
1.32-1.370.14531460.13362578X-RAY DIFFRACTION99.42
1.37-1.430.15161540.1232611X-RAY DIFFRACTION99.6
1.43-1.490.15241430.122605X-RAY DIFFRACTION99.85
1.49-1.570.14091270.11512653X-RAY DIFFRACTION99.93
1.57-1.670.14711350.11962625X-RAY DIFFRACTION99.46
1.67-1.80.14071340.12722658X-RAY DIFFRACTION99.93
1.8-1.980.16081220.12452636X-RAY DIFFRACTION99.86
1.98-2.270.13671250.13332669X-RAY DIFFRACTION100
2.27-2.850.16831560.15272644X-RAY DIFFRACTION99.82
2.85-44.980.16441590.15372697X-RAY DIFFRACTION99.76

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