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- PDB-4hr4: R2-like ligand-binding oxidase with anaerobically reconstituted m... -

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Basic information

Entry
Database: PDB / ID: 4hr4
TitleR2-like ligand-binding oxidase with anaerobically reconstituted metal cofactor
ComponentsRibonuleotide reductase small subunit
KeywordsOXIDOREDUCTASE / R2-like ligand-binding oxidase / heterodinuclear Mn/Fe cofactor / ribonucleotide reductase R2 subunit fold / metalloprotein / manganese / iron / fatty acid/long-chain hydrocarbon ligand
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
: / : / PALMITIC ACID / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.901 Å
AuthorsGriese, J.J. / Hogbom, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein
Authors: Griese, J.J. / Roos, K. / Cox, N. / Shafaat, H.S. / Branca, R.M.M. / Lehtio, J. / Graslund, A. / Lubitz, W. / Siegbahn, P.E.M. / Hogbom, M.
History
DepositionOct 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _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

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Assembly

Deposited unit
A: Ribonuleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3865
Polymers36,9631
Non-polymers4234
Water1,47782
1
A: Ribonuleotide reductase small subunit
hetero molecules

A: Ribonuleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,77210
Polymers73,9262
Non-polymers8468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7790 Å2
ΔGint-76 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.928, 97.709, 128.132
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-516-

HOH

21A-534-

HOH

31A-582-

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 (bacteria) / Strain: HTA246 / Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 48.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20%(w/v) PEG 1500, 0.1M HEPES-Na, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI 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: 1.9→50 Å / Num. all: 27657 / Num. obs: 27657 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 45.526 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.75
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.91 / Num. unique all: 4408 / % possible all: 98.7

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.901→48.855 Å / SU ML: 0.2 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 1383 5 %random
Rwork0.1809 ---
all0.1826 27653 --
obs0.1826 27653 98.52 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.7 Å2
Refinement stepCycle: LAST / Resolution: 1.901→48.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 21 82 2469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022458
X-RAY DIFFRACTIONf_angle_d1.3313330
X-RAY DIFFRACTIONf_dihedral_angle_d15.936910
X-RAY DIFFRACTIONf_chiral_restr0.078344
X-RAY DIFFRACTIONf_plane_restr0.007424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9009-1.96890.30091330.26342570270398
1.9689-2.04770.2721420.2442613275599
2.0477-2.14090.26561360.21612614275099
2.1409-2.25380.2521390.20472629276899
2.2538-2.3950.23261350.19572590272599
2.395-2.57990.24091430.18342638278199
2.5799-2.83950.25031350.19262608274398
2.8395-3.25030.23741370.19282616275398
3.2503-4.09470.19741370.16762637277497
4.0947-48.87060.17871460.15942755290198

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