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- PDB-4n82: X-ray crystal structure of Streptococcus sanguinis NrdIox -

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Basic information

Entry
Database: PDB / ID: 4n82
TitleX-ray crystal structure of Streptococcus sanguinis NrdIox
ComponentsRibonucleotide reductase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / RIBONUCLEOTIDE REDUCTASE / OXIDATION-REDUCTION / FLAVIN MONONUCLEOTIDE
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H / protein modification process / FMN binding
Similarity search - Function
Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / Flavodoxin domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Putative NrdI-like protein
Similarity search - Component
Biological speciesStreptococcus sanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsBoal, A.K. / Rosenzweig, A.C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS.
Authors: Makhlynets, O. / Boal, A.K. / Rhodes, D.V. / Kitten, T. / Rosenzweig, A.C. / Stubbe, J.
History
DepositionOct 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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_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
B: Ribonucleotide reductase
A: Ribonucleotide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2446
Polymers40,1392
Non-polymers1,1054
Water3,675204
1
B: Ribonucleotide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6223
Polymers20,0701
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Ribonucleotide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6223
Polymers20,0701
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.726, 56.612, 73.387
Angle α, β, γ (deg.)90.000, 106.130, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonucleotide reductase


Mass: 20069.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis (bacteria) / Strain: SK36 / Gene: nrdI, SSA_2263 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3CR20
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 4000, ammonium sulfate, pH 5.6, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 33395

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RLJ

1rlj


Resolution: 1.88→47.69 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.68 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1675 5 %RANDOM
Rwork0.2067 ---
obs0.2083 33340 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.85 Å2 / Biso mean: 33.6281 Å2 / Biso min: 16.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0.51 Å2
2--1.5 Å20 Å2
3----2.27 Å2
Refinement stepCycle: LAST / Resolution: 1.88→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 72 204 2681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.022539
X-RAY DIFFRACTIONr_angle_refined_deg1.0081.9993440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.725302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4724.88125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52815435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6171512
X-RAY DIFFRACTIONr_chiral_restr0.0670.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211918
LS refinement shellResolution: 1.884→1.933 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 105 -
Rwork0.265 2141 -
all-2246 -
obs--94.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9117-0.293-0.49720.8568-0.09680.8412-0.01150.0009-0.02430.1196-0.07330.014-0.08560.08550.08470.0698-0.0221-0.00510.05870.00760.0259-26.97726.001735.8093
20.56050.19811.46231.17881.06914.2024-0.02490.1935-0.00890.0216-0.0080.10250.02780.53260.03280.03130.01630.0060.14060.01110.017-18.357724.59173.9833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 154
2X-RAY DIFFRACTION2A2 - 154

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