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- PDB-5cns: Crystal structure of the dATP inhibited E. coli class Ia ribonucl... -

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Basic information

Entry
Database: PDB / ID: 5cns
TitleCrystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to CDP and dATP at 2.97 Angstroms resolution
Components(Ribonucleoside-diphosphate reductase 1 subunit ...) x 2
KeywordsOXIDOREDUCTASE / allostery / substrate specificity / ribonucleotide reductase / nucleotide metabolism
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, 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 / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-DIPHOSPHATE / 2'-DEOXYADENOSINE-5'-DIPHOSPHATE / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / MU-OXO-DIIRON / 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: 2.975 Å
AuthorsChen, P.Y.-T. / Zimanyi, C.M. / Funk, M.A. / Drennan, C.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)P30-ES002109 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM08334 United States
National Science Foundation (NSF, United States)0645960 United States
CitationJournal: Elife / Year: 2016
Title: Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli.
Authors: Zimanyi, C.M. / Chen, P.Y. / Kang, G. / Funk, M.A. / Drennan, C.L.
History
DepositionJul 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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

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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 alpha
E: Ribonucleoside-diphosphate reductase 1 subunit beta
F: Ribonucleoside-diphosphate reductase 1 subunit beta
G: Ribonucleoside-diphosphate reductase 1 subunit beta
H: Ribonucleoside-diphosphate reductase 1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)523,14332
Polymers517,2168
Non-polymers5,92724
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40700 Å2
ΔGint-324 kcal/mol
Surface area143320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)274.154, 157.830, 164.251
Angle α, β, γ (deg.)90.00, 118.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Ribonucleoside-diphosphate reductase 1 subunit ... , 2 types, 8 molecules ABCDEFGH

#1: Protein
Ribonucleoside-diphosphate reductase 1 subunit alpha / Protein B1 / Ribonucleoside-diphosphate reductase 1 R1 subunit / Ribonucleotide reductase 1


Mass: 85877.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: nrdA, dnaF, b2234, JW2228 / Production host: Escherichia coli (E. coli)
References: UniProt: P00452, ribonucleoside-diphosphate reductase
#2: Protein
Ribonucleoside-diphosphate reductase 1 subunit beta / Protein B2 / Protein R2 / Ribonucleotide reductase 1


Mass: 43426.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: nrdB, ftsB, b2235, JW2229 / Production host: Escherichia coli (E. coli)
References: UniProt: P69924, ribonucleoside-diphosphate reductase

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Non-polymers , 6 types, 167 molecules

#3: Chemical
ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#4: Chemical
ChemComp-DAT / 2'-DEOXYADENOSINE-5'-DIPHOSPHATE / DADP


Mass: 411.202 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O9P2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#7: Chemical
ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 9.5% (w/v) PEG 3350, 100 mM MOPS, 250 mM Mg(CH3COO)2, 25 mM 394 MgCl2, 5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.97→49.49 Å / Num. obs: 125630 / % possible obs: 98.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.093 / Net I/av σ(I): 13.9 / Net I/σ(I): 9.5
Reflection shellResolution: 2.97→3.08 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.527 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ERM

4erm


Resolution: 2.975→49.483 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 6187 5.02 %
Rwork0.1897 --
obs0.1909 123362 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.975→49.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34919 0 344 143 35406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00336127
X-RAY DIFFRACTIONf_angle_d0.63349022
X-RAY DIFFRACTIONf_dihedral_angle_d16.03421588
X-RAY DIFFRACTIONf_chiral_restr0.0415373
X-RAY DIFFRACTIONf_plane_restr0.0036282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9747-3.00850.33671730.3033186X-RAY DIFFRACTION80
3.0085-3.04390.32442250.29893970X-RAY DIFFRACTION99
3.0439-3.0810.32311990.28033893X-RAY DIFFRACTION100
3.081-3.120.29362210.26753930X-RAY DIFFRACTION99
3.12-3.1610.29332060.26783957X-RAY DIFFRACTION99
3.161-3.20430.271990.25013929X-RAY DIFFRACTION100
3.2043-3.25010.26951960.24883957X-RAY DIFFRACTION100
3.2501-3.29860.27612130.24873959X-RAY DIFFRACTION100
3.2986-3.35010.26522080.24093981X-RAY DIFFRACTION100
3.3501-3.4050.26042080.24353901X-RAY DIFFRACTION99
3.405-3.46370.27512240.23223925X-RAY DIFFRACTION100
3.4637-3.52670.24141920.22033965X-RAY DIFFRACTION100
3.5267-3.59450.23572070.22243948X-RAY DIFFRACTION100
3.5945-3.66780.21762200.20833959X-RAY DIFFRACTION99
3.6678-3.74760.23071980.19583961X-RAY DIFFRACTION99
3.7476-3.83470.20342250.18533875X-RAY DIFFRACTION99
3.8347-3.93060.21392200.18383955X-RAY DIFFRACTION99
3.9306-4.03680.22212060.18243925X-RAY DIFFRACTION99
4.0368-4.15550.20082040.17293958X-RAY DIFFRACTION99
4.1555-4.28960.1732010.16413931X-RAY DIFFRACTION99
4.2896-4.44280.18621800.15753947X-RAY DIFFRACTION99
4.4428-4.62060.1852190.15653912X-RAY DIFFRACTION99
4.6206-4.83070.18872190.15563921X-RAY DIFFRACTION98
4.8307-5.08510.17682020.15853928X-RAY DIFFRACTION98
5.0851-5.40340.19271870.17253912X-RAY DIFFRACTION98
5.4034-5.820.21472200.1793919X-RAY DIFFRACTION98
5.82-6.40460.1861910.18173889X-RAY DIFFRACTION98
6.4046-7.32870.19791780.16563927X-RAY DIFFRACTION97
7.3287-9.22370.15972200.14083887X-RAY DIFFRACTION97
9.2237-49.48940.17632260.15523868X-RAY DIFFRACTION95

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