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- PDB-2xo4: RIBONUCLEOTIDE REDUCTASE Y730NH2Y MODIFIED R1 SUBUNIT OF E. COLI -

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Basic information

Entry
Database: PDB / ID: 2xo4
TitleRIBONUCLEOTIDE REDUCTASE Y730NH2Y MODIFIED R1 SUBUNIT OF E. COLI
Components
  • RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
  • RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
KeywordsOXIDOREDUCTASE / NUCLEOTIDE-BINDING / ALTERNATIVE INITIATION / DNA REPLICATION / ALLOSTERIC ENZYME
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 / protein folding chaperone / iron ion binding / ATP binding ...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 / protein folding chaperone / iron ion binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal ...ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / 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-like / Ferritin-like superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase 1 subunit alpha / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMinnihan, E.C. / Seyedsayamdost, M.R. / Uhlin, U. / Stubbe, J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2011
Title: Kinetics of Radical Intermediate Formation and Deoxynucleotide Production in 3-Aminotyrosine- Substituted Escherichia Coli Ribonucleotide Reductases.
Authors: Minnihan, E.C. / Seyedsayamdost, M.R. / Uhlin, U. / Stubbe, J.
#1: Journal: Nature / Year: 1994
Title: Structure of Ribonucleotide Reductase Protein R1
Authors: Uhlin, U. / Eklund, H.
#2: Journal: Structure / Year: 1997
Title: Binding of Allosteric Effectors to Ribonucleotide Reductase Protein R1: Reduction of Active-Site Cysteines Promotes Substrate Binding
Authors: Eriksson, M. / Uhlin, U. / Ramaswamy, S. / Ekberg, M. / Regnstrom, K. / Sjoberg, B.M. / Eklund, H.
History
DepositionAug 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
C: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
D: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
E: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
F: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
P: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA


Theoretical massNumber of molelcules
Total (without water)266,7627
Polymers266,7627
Non-polymers00
Water18,1411007
1
C: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
F: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
x 6


Theoretical massNumber of molelcules
Total (without water)528,98112
Polymers528,98112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation6_555-x,-x+y,-z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area28920 Å2
ΔGint-156.4 kcal/mol
Surface area156380 Å2
MethodPISA
2
A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
D: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
E: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA

A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
D: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
E: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA

A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
D: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
E: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA


Theoretical massNumber of molelcules
Total (without water)528,98112
Polymers528,98112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area29660 Å2
ΔGint-152.1 kcal/mol
Surface area156060 Å2
MethodPISA
3
P: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA


  • defined by software
  • 2.27 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,2711
Polymers2,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)224.592, 224.592, 336.719
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-2150-

HOH

21C-2252-

HOH

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Components

#1: Protein RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA / RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 R1 SUBUNIT / RIBONUCLEOTIDE REDUCTASE 1 / PROTEIN B1 / ...RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 R1 SUBUNIT / RIBONUCLEOTIDE REDUCTASE 1 / PROTEIN B1 / RIBONUCLEOTIDE REDUCTASE R1 SUBUNIT


Mass: 85892.102 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-761
Source method: isolated from a genetically manipulated source
Details: SITE SPECIFIC INCORPORATION OF 3-AMINOTYROSINE AT POSITION 730
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PBADMYCHISA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10
References: UniProt: P00452, ribonucleoside-diphosphate reductase
#2: Protein/peptide
RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA / RIBONUCLEOTIDE REDUCTASE 1 / PROTEIN B2 / PROTEIN R2


Mass: 2271.392 Da / Num. of mol.: 4
Fragment: RIBONUCLEOTIDE REDUCTASE R2-PEPTIDE, RESIDUES 357-376
Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
References: UniProt: P69924, ribonucleoside-diphosphate reductase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1007 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.07 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 6
Details: LITHIUM SULPHATE 1.5M, SODIUM CHLORIDE BUFFER PH 6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→84.21 Å / Num. obs: 112261 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 4.47 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.52 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.94 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X0X

2x0x


Resolution: 2.5→169.031 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.084 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.376 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PO4 PO4 BINDING LOOP CONTAINING RESIDUES 268-273 ARE DISORDERED. STRONG INDICATION THAT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PO4 PO4 BINDING LOOP CONTAINING RESIDUES 268-273 ARE DISORDERED. STRONG INDICATION THAT Y731 AND N733 HAVE TWO POSITIONS. THE SECOND POSITION FOR THESE RESIDUES ARE BUILT IN MOLECULE C. THE 11-16 C-TERMINAL RESIDUES OF THE R2 PEPTIDE, CHAINS D, E, F BIND AT THE R2 BINDING-SITE OF THE R1 MOLECULES, CHAINS A, B, C. THE THREE N-TERMINAL RESIDUES, UNIQUE CHAIN P, ARE SITUATED BETWEEN MOL A AND C. THIS LATTER BINDING HAS NO KNOWN BIOLOGICAL RELEVANCE BUT IS ESSENTIAL FOR CRYSTAL LATTICE FORMATION. WATERS CLOSE TO SER 625 MAY REPRESENT A SULPHATE ION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 5622 5.08 %RANDOM
Rwork0.1884 ---
obs0.191 112260 99.962 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.867 Å2
Baniso -1Baniso -2Baniso -3
1-0.177 Å20.089 Å20 Å2
2--0.177 Å20 Å2
3----0.266 Å2
Refinement stepCycle: LAST / Resolution: 2.5→169.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17952 0 0 1007 18959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02218336
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.96324837
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57352246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94124.117889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.539153151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.16815120
X-RAY DIFFRACTIONr_chiral_restr0.0840.22729
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214014
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.28920
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.212564
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.21141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.561.511504
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.014218073
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.237707
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0454.56764
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 415 -
Rwork0.281 7807 -
obs--99.988 %

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