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- PDB-1rlj: Structural Genomics, a Flavoprotein NrdI from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1rlj
TitleStructural Genomics, a Flavoprotein NrdI from Bacillus subtilis
ComponentsNrdI protein
KeywordsStructural Genomics / unknown function / Flavoprotein / FMN / Thioredoxin / Alpha/beta/alpha sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


protein modification process => GO:0036211 / FMN binding
Similarity search - Function
Ribonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / IODIDE ION / Protein NrdI
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWu, R. / Zhang, R. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.5A crystal structure of a thioredoxin-like protein NrdI from Bacillus subtilis
Authors: Wu, R. / Zhang, R. / Collart, F. / Joachimiak, A.
History
DepositionNov 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NrdI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3984
Polymers15,6881
Non-polymers7103
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.236, 85.236, 59.992
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
DetailsThis protein exists as monomer.

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Components

#1: Protein NrdI protein


Mass: 15687.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: NRDI, BSU17370 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P50618
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 4.01 Å3/Da / Density % sol: 69.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.2M NH4I, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97835 Å
DetectorType: SBC-2 / Detector: CCD / Date: Nov 19, 2003 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97835 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 32842 / Num. obs: 32842 / % possible obs: 100 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 6.24 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 24.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.79 / Num. unique all: 3311 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→42.62 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 282129.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1602 5 %RANDOM
Rwork0.192 ---
obs0.192 31905 96.9 %-
all-32842 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.5754 Å2 / ksol: 0.387085 e/Å3
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-0.48 Å20 Å2
2---2.08 Å20 Å2
3---4.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 33 132 1239
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2476 298 6 %
Rwork0.2424 4708 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4FMN.PARAM

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