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- PDB-4xbw: R2-like ligand-binding oxidase with aerobically reconstituted dim... -

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Basic information

Entry
Database: PDB / ID: 4xbw
TitleR2-like ligand-binding oxidase with aerobically reconstituted dimanganese cofactor
ComponentsRibonucleotide reductase small subunit
KeywordsOXIDOREDUCTASE / R2-like ligand-binding oxidase / dimanganese cofactor / ribonucleotide reductase R2 subunit fold / metalloprotein
Function / homology
Function and homology information


deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
R2-like ligand binding oxidase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PALMITIC ACID / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.991 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
DepositionDec 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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)37,3845
Polymers36,9631
Non-polymers4214
Water95553
1
A: Ribonucleotide reductase small subunit
hetero molecules

A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,76810
Polymers73,9262
Non-polymers8428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5370 Å2
ΔGint-42 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.374, 97.153, 128.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21A-509-

HOH

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Components

#1: Protein Ribonucleotide reductase small subunit / R2-LIKE LIGAND-BINDING OXIDASE


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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22.5 % (w/v) PEG1500, 0.1 M HEPES-Na, pH 7.0, 22.5 % (w/v) PEG1500, 0.1 M HEPES-Na, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 3, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 24406 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 38.12 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 21.93
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 1.92 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1606)refinement
XDSdata reduction
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4HR4

4hr4


Resolution: 1.991→48.76 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1222 5.01 %random selection
Rwork0.1773 ---
obs0.1796 24403 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.4 Å2
Refinement stepCycle: LAST / Resolution: 1.991→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 21 53 2344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222355
X-RAY DIFFRACTIONf_angle_d1.3133161
X-RAY DIFFRACTIONf_dihedral_angle_d16.022876
X-RAY DIFFRACTIONf_chiral_restr0.061330
X-RAY DIFFRACTIONf_plane_restr0.008407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9914-2.07110.31791320.27512521X-RAY DIFFRACTION98
2.0711-2.16540.27111340.24412541X-RAY DIFFRACTION100
2.1654-2.27960.25921320.20312539X-RAY DIFFRACTION100
2.2796-2.42240.21281370.19112545X-RAY DIFFRACTION100
2.4224-2.60940.22351360.18232568X-RAY DIFFRACTION100
2.6094-2.8720.24861330.18462576X-RAY DIFFRACTION100
2.872-3.28750.22771380.19222589X-RAY DIFFRACTION100
3.2875-4.14150.20271370.16612609X-RAY DIFFRACTION100
4.1415-48.77440.21441430.15282693X-RAY DIFFRACTION98

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