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- PDB-1pim: DITHIONITE REDUCED E. COLI RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT, D... -

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Basic information

Entry
Database: PDB / ID: 1pim
TitleDITHIONITE REDUCED E. COLI RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT, D84E MUTANT
ComponentsRibonucleoside-diphosphate reductase 1 beta chain
KeywordsOXIDOREDUCTASE / four-helix bundle / diiron cluster / diferrous cluster
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / 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: 2 Å
AuthorsVoegtli, W.C. / Khidekel, N. / Baldwin, J. / Ley, B.A. / Bollinger Jr., J.M. / Rosenzweig, A.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2000
Title: Crystal Structure of the Ribonucleotide Reductase R2 Mutant that Accumulates a u-1,2-Peroxodiiron(III) Intermediate during Oxygen Activation
Authors: Voegtli, W.C. / Khidekel, N. / Baldwin, J. / Ley, B.A. / Bollinger Jr., J.M. / Rosenzweig, A.C.
History
DepositionMay 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQRES Author states the conflict with residue 326 is not a an engineered mutation, but possibly a ...SEQRES Author states the conflict with residue 326 is not a an engineered mutation, but possibly a modelling error in the molecular search object, which was not changed in the final model.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)88,48113
Polymers86,8542
Non-polymers1,62811
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-265 kcal/mol
Surface area24520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.100, 84.600, 114.800
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 chains

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Components

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


Mass: 43426.863 Da / Num. of mol.: 2 / Mutation: D84E
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.: 7 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
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 ℃ / 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
5200 mM1reservoirNaCl
620 %PEG40001reservoir
70.3 %dioxane1reservoir
81 mMEMTS1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.0045 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 1998
RadiationMonochromator: Double crystal, Daresbury type / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0045 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 49439 / Num. obs: 47987 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.5 Å2
Reflection shellResolution: 2→2.13 Å / % possible all: 94.4
Reflection
*PLUS
Highest resolution: 1.98 Å / Lowest resolution: 35 Å / Num. obs: 49651 / % possible obs: 98.7 % / Num. measured all: 480461 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.298

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Diferric wildtype ribonucleotide reductase R2 without metal ions or solvent molecules

Resolution: 2→23.75 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 633079.59 / Data cutoff high rms absF: 633079.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Iron atoms refined as Fe(II) ions
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2411 5 %RANDOM
Rwork0.204 ---
all0.207 47987 --
obs0.204 47987 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.5253 Å2 / ksol: 0.401352 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.65 Å20 Å20 Å2
2--1.25 Å20 Å2
3---5.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→23.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 11 202 5783
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it2.611.5
X-RAY DIFFRACTIONc_mcangle_it3.392
X-RAY DIFFRACTIONc_scbond_it4.182
X-RAY DIFFRACTIONc_scangle_it5.732.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 394 5.1 %
Rwork0.249 7293 -
obs-7293 94.4 %
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
Highest resolution: 1.98 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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