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- PDB-4xb9: R2-like ligand-binding oxidase with aerobically reconstituted dii... -

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Basic information

Entry
Database: PDB / ID: 4xb9
TitleR2-like ligand-binding oxidase with aerobically reconstituted diiron cofactor
ComponentsRibonuleotide reductase small subunit
KeywordsOXIDOREDUCTASE / R2-like ligand-binding oxidase / diiron 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 / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsGriese, J.J. / Hogbom, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Sweden
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 16, 2014Deposition 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3314
Polymers36,9631
Non-polymers3683
Water1,802100
1
A: Ribonuleotide reductase small subunit
hetero molecules

A: Ribonuleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6628
Polymers73,9262
Non-polymers7366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7550 Å2
ΔGint-80 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.044, 97.053, 129.742
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-514-

HOH

21A-517-

HOH

31A-525-

HOH

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Components

#1: Protein Ribonuleotide 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
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#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.: 100 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% (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: 0.918 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: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.798→50 Å / Num. obs: 33183 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 30.24 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 18.94
Reflection shellResolution: 1.798→1.91 Å / Redundancy: 4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.14 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1606)refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HR0

4hr0


Resolution: 1.798→48.533 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 1659 5 %random selection
Rwork0.1645 ---
obs0.1664 33179 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.3 Å2
Refinement stepCycle: LAST / Resolution: 1.798→48.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 20 100 2477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162451
X-RAY DIFFRACTIONf_angle_d1.2643292
X-RAY DIFFRACTIONf_dihedral_angle_d15.612910
X-RAY DIFFRACTIONf_chiral_restr0.055344
X-RAY DIFFRACTIONf_plane_restr0.007424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7978-1.85070.28751340.25622534X-RAY DIFFRACTION99
1.8507-1.91050.29311390.22792622X-RAY DIFFRACTION100
1.9105-1.97880.22281350.20812600X-RAY DIFFRACTION100
1.9788-2.0580.24971360.19462586X-RAY DIFFRACTION100
2.058-2.15160.20491390.18042626X-RAY DIFFRACTION100
2.1516-2.26510.21661370.17292614X-RAY DIFFRACTION100
2.2651-2.4070.17131360.15972610X-RAY DIFFRACTION100
2.407-2.59280.19621390.15482649X-RAY DIFFRACTION100
2.5928-2.85370.23071390.16482629X-RAY DIFFRACTION100
2.8537-3.26660.23071380.17112627X-RAY DIFFRACTION100
3.2666-4.11520.18051390.15532663X-RAY DIFFRACTION99
4.1152-48.55090.18171480.14712760X-RAY DIFFRACTION98

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