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- PDB-2xaz: Ribonucleotide reductase Y730NO2Y and C439S modified R1 subunit o... -

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Basic information

Entry
Database: PDB / ID: 2xaz
TitleRibonucleotide reductase Y730NO2Y and C439S modified R1 subunit of E. coli
Components
  • RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHARibonucleotide reductase
  • RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETARibonucleotide reductase
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 / DNA replication / iron ion 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 / DNA replication / iron ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / 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, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / 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 / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / 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: 2.6 Å
AuthorsYokoyama, K. / Uhlin, U. / Stubbe, J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2010
Title: Site-Specific Incorporation of 3-Nitrotyrosine as a Probe of Pk(A) Perturbation of Redox-Active Tyrosines in Ribonucleotide Reductase.
Authors: Yokoyama, K. / 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
DepositionApr 1, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionApr 14, 2010ID: 2X59
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 20, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / struct_biol / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_database_status.recvd_author_approval / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)266,8047
Polymers266,8047
Non-polymers00
Water6,287349
1
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)529,06412
Polymers529,06412
Non-polymers00
Water1086
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 area24870 Å2
ΔGint-138.3 kcal/mol
Surface area154440 Å2
MethodPISA
2
C: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
F: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
x 6


Theoretical massNumber of molelcules
Total (without water)529,06412
Polymers529,06412
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 area25570 Å2
ΔGint-142 kcal/mol
Surface area154840 Å2
MethodPISA
3
P: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA


  • defined by author&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)224.807, 224.807, 337.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA / Ribonucleotide reductase / 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: 85906.023 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-761 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SITE SPECIFIC INCORPORATION OF 3-NITROTYROSINE 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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 439 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 439 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 439 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 439 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 439 TO SER

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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: 3.23 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 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.6→84.21 Å / Num. obs: 96638 / % possible obs: 96.6 % / Observed criterion σ(I): -3.7 / Redundancy: 3.72 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.69
Reflection shellResolution: 2.6→2.62 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.06 / % possible all: 97.7

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Processing

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

2x0x


Resolution: 2.6→169.031 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.026 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.51 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 268-273 ARE DISORDERED. THE 11-16 C-TERMINAL RESIDUES OF THE R2 PEPTIDE, CHAINS D, E, F, BIND AT THE R2 BINDING-SITE OF THE R1 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 268-273 ARE DISORDERED. 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 NEEDED FOR CRYSTAL-LATTICE FORMATION. WATERS CLOSE TO SER 625 MAY REPRESENT A SULPHATE ION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 4825 5.03 %RANDOM
Rwork0.1961 ---
obs0.199 96638 96.405 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.616 Å2
Baniso -1Baniso -2Baniso -3
1-0.241 Å20.12 Å20 Å2
2--0.241 Å20 Å2
3----0.361 Å2
Refinement stepCycle: LAST / Resolution: 2.6→169.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17795 0 0 349 18144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02218176
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.231.96324621
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74752220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54724.125880
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.958153122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.74415117
X-RAY DIFFRACTIONr_chiral_restr0.0870.22708
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213883
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.28263
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.212533
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2745
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5781.511349
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.052217897
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2837665
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1654.56724
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: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 338 -
Rwork0.314 6851 -
obs--97.783 %

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