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- PDB-1piy: RIBONUCLEOTIDE REDUCTASE R2 SOAKED WITH FERROUS ION AT NEUTRAL PH -

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Basic information

Entry
Database: PDB / ID: 1piy
TitleRIBONUCLEOTIDE REDUCTASE R2 SOAKED WITH FERROUS ION AT NEUTRAL PH
ComponentsRibonucleoside-diphosphate reductase 1 beta chain
KeywordsOXIDOREDUCTASE / Four-helix bundle / diferrous cluster
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / 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
: / : / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsVoegtli, W.C. / Sommerhalter, M. / Saleh, L. / Baldwin, J. / Bollinger Jr., J.M. / Rosenzweig, A.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Variable coordination geometries at the diiron(II) active site of ribonucleotide reductase R2.
Authors: Voegtli, W.C. / Sommerhalter, M. / Saleh, L. / Baldwin, J. / Bollinger Jr., J.M. / Rosenzweig, A.C.
History
DepositionMay 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONFLICTS ARE DUE TO A MODELLING ERROR IN THE INITIAL MODEL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase 1 beta chain
B: Ribonucleoside-diphosphate reductase 1 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,85720
Polymers86,8262
Non-polymers3,03218
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-323 kcal/mol
Surface area23930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.900, 84.600, 114.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTetramer of two alpha and two beta subunits

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Components

#1: Protein Ribonucleoside-diphosphate reductase 1 beta chain / Ribonucleotide reductase 1 / B2 protein / R2 protein


Mass: 43412.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RIR2 / Production host: Escherichia coli (E. coli)
References: UniProt: P69924, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 4000, 200mM NaCl, 50mM MES, 0.3% dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMHEPES1droppH7.6
31 mMEMTS1drop
450 mMMES1reservoirpH6.0
520 %(w/v)PEG40001reservoir
6200 mM1reservoirNaCl
71 mMEMTS1reservoir
80.5 %(w/v)dioxane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.68→25 Å / Num. all: 82056 / Num. obs: 78137 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.6 Å2
Reflection shellResolution: 1.68→1.79 Å / % possible all: 89.1
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 80287 / % possible obs: 97.8 % / Num. measured all: 1103745 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PIM

1pim


Resolution: 1.68→24.08 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1901059.32 / Data cutoff high rms absF: 1901059.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3938 5 %RANDOM
Rwork0.225 ---
all0.229 78137 --
obs0.225 78137 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4452 Å2 / ksol: 0.38937 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.16 Å20 Å20 Å2
2--3.65 Å20 Å2
3----0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.68→24.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 18 248 5832
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it0.171.5
X-RAY DIFFRACTIONc_mcangle_it0.322
X-RAY DIFFRACTIONc_scbond_it0.172
X-RAY DIFFRACTIONc_scangle_it0.272.5
LS refinement shellResolution: 1.68→1.79 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 576 4.8 %
Rwork0.264 11424 -
obs-11424 89.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3TOPPER_ION.PARAMTOPPER_ION.TOP
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection obs: 77979 / % reflection Rfree: 5 % / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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