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- PDB-1r65: Crystal structure of ferrous soaked Ribonucleotide Reductase R2 s... -

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Basic information

Entry
Database: PDB / ID: 1r65
TitleCrystal structure of ferrous soaked Ribonucleotide Reductase R2 subunit (wildtype) at pH 5 from E. coli
ComponentsRibonucleoside-diphosphate reductase 1 beta chain
KeywordsOXIDOREDUCTASE
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: 1.95 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
DepositionOct 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 14, 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_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 AUTHORS SAY THE MISMATCH AT RESIDUE 326 IS AN ERROR IN BUILDING THE 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)89,65719
Polymers86,8262
Non-polymers2,83117
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-326 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.170, 84.220, 114.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Fragment: Ribonucleotide Reductase R2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NRDB, FTSB, B2235, Z3491, ECS3118 / Production host: Escherichia coli (E. coli)
References: UniProt: P69924, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Fragment: Ribonucleotide Reductase R2 / Mutation: none / Source method: obtained synthetically / Formula: Fe / References: ribonucleoside-diphosphate reductase
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 40.11 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG4000, sodium chloride, EMTS, MES, pH 6, 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: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.078 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 51995 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.108 / Net I/σ(I): 16.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 5067 / Rsym value: 0.415 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 228122 / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.415

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→25 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
Details: Residue 7 is missing side chain density. Residues 341-375 were missing in the electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 5099 -random
Rwork0.207 ---
all-50619 --
obs-50619 95.8 %-
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.768 Å20 Å20 Å2
2---8.801 Å20 Å2
3---3.033 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 17 197 5780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_dehedral_angle_deg18.9
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.304 751 -
Rwork0.268 --
obs-6596 84.9 %
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.1

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