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- PDB-2xo5: RIBONUCLEOTIDE REDUCTASE Y731NH2Y MODIFIED R1 SUBUNIT OF E. COLI -

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Basic information

Entry
Database: PDB / ID: 2xo5
TitleRIBONUCLEOTIDE REDUCTASE Y731NH2Y MODIFIED R1 SUBUNIT OF E. COLI
Components
  • RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
  • RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
KeywordsOXIDOREDUCTASE / NUCLEOTIDE BINDING
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 / cytosol / cytoplasm
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: 2.7 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water16,250902
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 area27090 Å2
ΔGint-159 kcal/mol
Surface area153450 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 area27530 Å2
ΔGint-145 kcal/mol
Surface area153370 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)223.238, 223.238, 335.665
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-2132-

HOH

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Components

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


Mass: 85892.102 Da / Num. of mol.: 3 / Fragment: CATALYTIC SUBUNIT, RESIDUES 1-761
Source method: isolated from a genetically manipulated source
Details: SITE SPECIFIC INCORPORATION OF 3-AMINOTYROSINE AT POSITION 731
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PBADMYCHISA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TOP10
References: UniProt: P00452, ribonucleoside-diphosphate reductase
#2: Protein/peptide
RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA / R2 PEPTIDE / RIBONUCLEOTIDE REDUCTASE 1 / PROTEIN B2 / PROTEIN R2


Mass: 2271.392 Da / Num. of mol.: 4 / Fragment: R1 BINDING PEPTIDE / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: P69924
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 902 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details3-AMINOTYROSINE (TY2): SITE SPECIFIC MODIFICATION OF 3-AMINOTYROSINE AT POSITION 731

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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: 3.04 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: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.7→79.06 Å / Num. obs: 87927 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 5.62 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.11
Reflection shellResolution: 2.7→2.72 Å / Redundancy: 5.64 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.88 / % 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: 2.7→166.667 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.306 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.742 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PO4 BINDING LOOP CONTAINING RESIDUES 268-273 IS DISORDERED. POSITION OF THE NH2 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PO4 BINDING LOOP CONTAINING RESIDUES 268-273 IS DISORDERED. POSITION OF THE NH2 MODIFICATION DIFFER IN MOLECULE B. 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
Rfree0.2283 4407 5.02 %RANDOM
Rwork0.1768 ---
obs0.179 87922 99.923 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.993 Å2
Baniso -1Baniso -2Baniso -3
1--0.355 Å2-0.177 Å20 Å2
2---0.355 Å20 Å2
3---0.532 Å2
Refinement stepCycle: LAST / Resolution: 2.7→166.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17952 0 0 902 18854
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_deg1.2241.96324837
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96352246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03124.117889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7153151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.14315120
X-RAY DIFFRACTIONr_chiral_restr0.0920.22729
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214014
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.29641
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.212636
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.21164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3540.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5921.511454
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.075218073
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.25237715
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1544.56764
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 321 -
Rwork0.27 6088 -
obs--99.984 %

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