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

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Basic information

Entry
Database: PDB / ID: 5cnt
TitleCrystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to UDP and dATP at 3.25 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / MU-OXO-DIIRON / URIDINE-5'-DIPHOSPHATE / 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: 3.25 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 1.2Aug 23, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_detector / pdbx_struct_oper_list / software
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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)525,43236
Polymers517,2168
Non-polymers8,21628
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42530 Å2
ΔGint-308 kcal/mol
Surface area142260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)274.621, 157.340, 165.200
Angle α, β, γ (deg.)90.00, 119.30, 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 , 5 types, 87 molecules

#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-FEO / MU-OXO-DIIRON


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


Mass: 18.015 Da / Num. of mol.: 59 / 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: 59.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% (w/v) PEG 3350, 100 mM MOPS pH 7.5, 300 mM Mg(CH3COO)2, 30 mM MgCl2, and 5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.24→49.95 Å / Num. obs: 96695 / % possible obs: 98.8 % / Redundancy: 3.9 % / Rsym value: 0.096 / Net I/av σ(I): 13.1 / Net I/σ(I): 10.7
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.3 / % possible all: 99.2

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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: 3.25→49.95 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2207 4757 5 %
Rwork0.1924 --
obs0.1939 95095 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34898 0 480 59 35437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00336249
X-RAY DIFFRACTIONf_angle_d0.65149153
X-RAY DIFFRACTIONf_dihedral_angle_d15.71121641
X-RAY DIFFRACTIONf_chiral_restr0.0415378
X-RAY DIFFRACTIONf_plane_restr0.0036279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.2870.33391550.30372874X-RAY DIFFRACTION95
3.287-3.32560.30891460.27993013X-RAY DIFFRACTION99
3.3256-3.36620.29961600.27093048X-RAY DIFFRACTION100
3.3662-3.40880.29031740.26682966X-RAY DIFFRACTION99
3.4088-3.45360.28871730.2713026X-RAY DIFFRACTION99
3.4536-3.50090.2991370.26813003X-RAY DIFFRACTION99
3.5009-3.55090.31161520.26322988X-RAY DIFFRACTION98
3.5509-3.60390.321550.25392932X-RAY DIFFRACTION96
3.6039-3.66020.25111650.23242992X-RAY DIFFRACTION99
3.6602-3.72020.25491670.23152977X-RAY DIFFRACTION99
3.7202-3.78430.26211470.21643088X-RAY DIFFRACTION100
3.7843-3.85310.24881830.20863031X-RAY DIFFRACTION100
3.8531-3.92720.22911550.2013002X-RAY DIFFRACTION99
3.9272-4.00730.23821590.20673014X-RAY DIFFRACTION100
4.0073-4.09440.241550.1993052X-RAY DIFFRACTION100
4.0944-4.18960.25511630.19443032X-RAY DIFFRACTION100
4.1896-4.29430.18781500.18372987X-RAY DIFFRACTION98
4.2943-4.41040.22541420.17882984X-RAY DIFFRACTION97
4.4104-4.54010.2041480.1712993X-RAY DIFFRACTION98
4.5401-4.68650.19111610.16833037X-RAY DIFFRACTION99
4.6865-4.85390.1841780.16513019X-RAY DIFFRACTION99
4.8539-5.0480.20491540.16663039X-RAY DIFFRACTION100
5.048-5.27750.20161620.17953042X-RAY DIFFRACTION99
5.2775-5.55540.23161510.18553026X-RAY DIFFRACTION99
5.5554-5.9030.19561570.18132942X-RAY DIFFRACTION96
5.903-6.35790.21181460.18883070X-RAY DIFFRACTION99
6.3579-6.99620.19041380.17053065X-RAY DIFFRACTION100
6.9962-8.0050.18951570.16443070X-RAY DIFFRACTION99
8.005-10.07180.14781850.13512963X-RAY DIFFRACTION97
10.0718-49.95610.20991820.17143063X-RAY DIFFRACTION98

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