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- PDB-5dcs: R2-like ligand-binding oxidase with aerobically reconstituted Mn/... -

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Basic information

Entry
Database: PDB / ID: 5dcs
TitleR2-like ligand-binding oxidase with aerobically reconstituted Mn/Fe cofactor (long soak)
ComponentsRibonucleotide reductase small subunit
KeywordsOXIDOREDUCTASE / R2-LIKE LIGAND-BINDING OXIDASE / DIIRON COFACTOR / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FOLD / METALLOPROTEIN OXIDOREDUCTASE
Function / homology
Function and homology information


deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
R2-like ligand binding oxidase / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / MANGANESE (III) ION / PALMITIC ACID / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsGriese, J.J. / Hogbom, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor.
Authors: Griese, J.J. / Kositzki, R. / Schrapers, P. / Branca, R.M. / Nordstrom, A. / Lehtio, J. / Haumann, M. / Hogbom, M.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3855
Polymers36,9631
Non-polymers4224
Water1,11762
1
A: Ribonucleotide reductase small subunit
hetero molecules

A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,77010
Polymers73,9262
Non-polymers8448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7780 Å2
ΔGint-67 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.058, 97.419, 129.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

21A-526-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ribonucleotide reductase small subunit


Mass: 36962.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria)
Strain: HTA426 / Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase

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Non-polymers , 5 types, 66 molecules

#2: Chemical ChemComp-MN3 / MANGANESE (III) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 22.5% (w/v) PEG 1500, 0.1 M HEPES-Na pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2012
RadiationMonochromator: Si(111) monochromator and Rh mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.006→50 Å / Num. obs: 23996 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 5.35
Reflection shellResolution: 2.006→2.13 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 1.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HR0

4hr0


Resolution: 2.006→38.906 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 20.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 1197 4.99 %random selection
Rwork0.1692 ---
obs0.1716 23992 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.1 Å2
Refinement stepCycle: LAST / Resolution: 2.006→38.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 21 62 2460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172477
X-RAY DIFFRACTIONf_angle_d1.2163354
X-RAY DIFFRACTIONf_dihedral_angle_d15.757921
X-RAY DIFFRACTIONf_chiral_restr0.057346
X-RAY DIFFRACTIONf_plane_restr0.007428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0056-2.08580.2791300.21792483X-RAY DIFFRACTION99
2.0858-2.18080.23691310.19582474X-RAY DIFFRACTION100
2.1808-2.29570.24581330.18382501X-RAY DIFFRACTION99
2.2957-2.43950.22711320.17292526X-RAY DIFFRACTION99
2.4395-2.62790.23221300.17022493X-RAY DIFFRACTION100
2.6279-2.89220.22461350.17562543X-RAY DIFFRACTION100
2.8922-3.31060.25211330.18342539X-RAY DIFFRACTION99
3.3106-4.17020.20911320.16022559X-RAY DIFFRACTION100
4.1702-38.91290.1861410.15662677X-RAY DIFFRACTION99

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