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- PDB-4r1r: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH SUBSTRATE, GDP AND EFFEC... -

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Basic information

Entry
Database: PDB / ID: 4r1r
TitleRIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH SUBSTRATE, GDP AND EFFECTOR DTTP FROM ESCHERICHIA COLI
Components
  • RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
  • RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
KeywordsCOMPLEX (OXIDOREDUCTASE/PEPTIDE) / RIBONUCLEOTIDE REDUCTASE / DEOXYRIBONUCLEOTIDE SYNTHESIS / RADICAL CHEMISTRY / ALLOSTERIC REGULATION / SPECIFICITY / COMPLEX (OXIDOREDUCTASE-PEPTIDE) / COMPLEX (OXIDOREDUCTASE-PEPTIDE) complex
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
GUANOSINE-5'-DIPHOSPHATE / THYMIDINE-5'-TRIPHOSPHATE / Ribonucleoside-diphosphate reductase 1 subunit alpha / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / RIGID BODY / Resolution: 3.2 Å
AuthorsEriksson, M. / Eklund, H.
Citation
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.
#1: Journal: Nature / Year: 1994
Title: Structure of Ribonucleotide Reductase Protein R1
Authors: Uhlin, U. / Eklund, H.
History
DepositionJul 22, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
P: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,39713
Polymers266,6217
Non-polymers2,7766
Water00
1
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
P: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3135
Polymers90,3883
Non-polymers9252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0424
Polymers88,1162
Non-polymers9252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-23 kcal/mol
Surface area28980 Å2
MethodPISA
3
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0424
Polymers88,1162
Non-polymers9252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-23 kcal/mol
Surface area28990 Å2
MethodPISA
4
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
P: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
P: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
P: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,06527
Polymers535,51315
Non-polymers5,55212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area38270 Å2
ΔGint-196 kcal/mol
Surface area155520 Å2
MethodPISA
5
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)534,25124
Polymers528,69812
Non-polymers5,55212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area36360 Å2
ΔGint-189 kcal/mol
Surface area155640 Å2
MethodPISA
6
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
P: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,3559
Polymers178,5045
Non-polymers1,8514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-53 kcal/mol
Surface area55010 Å2
MethodPISA
7
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules

C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,0848
Polymers176,2334
Non-polymers1,8514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area9050 Å2
ΔGint-50 kcal/mol
Surface area54950 Å2
MethodPISA
8
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)534,25124
Polymers528,69812
Non-polymers5,55212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area36800 Å2
ΔGint-188 kcal/mol
Surface area155110 Å2
MethodPISA
9
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,0848
Polymers176,2334
Non-polymers1,8514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-50 kcal/mol
Surface area54880 Å2
MethodPISA
10
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0424
Polymers88,1162
Non-polymers9252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-23 kcal/mol
Surface area28980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.020, 224.020, 335.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9084, 0.4181, 0.0034), (0.4181, 0.9084, 0.0006), (-0.0028, 0.002, -1)-54.269, 11.6517, -6.8774
2given(-0.7349, 0.6781, -0.0052), (-0.6781, -0.7349, -0.0008), (-0.0044, 0.0029, 1)-87.6897, 95.0882, 3.0033

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Components

#1: Protein RIBONUCLEOTIDE REDUCTASE R1 PROTEIN


Mass: 85845.023 Da / Num. of mol.: 3 / Mutation: C292A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NRDA / Production host: Escherichia coli (E. coli)
References: UniProt: P00452, ribonucleoside-diphosphate reductase
#2: Protein/peptide
RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Mass: 2271.392 Da / Num. of mol.: 4 / Fragment: C-TERMINAL PORTION, 20 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P69924
#3: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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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: 56.5 %
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 1.7 M LITHIUM SULFATE, AND 10 MM MAGNESIUM SULFATE IN 25 MM CITRATE BUFFER AT PH 6.0. THE PROTEIN SOLUTION CONTAINED 17 MG/ML R1 PROTEIN, 20-FOLD EXCESS FO A 20- ...Details: PROTEIN WAS CRYSTALLIZED FROM 1.7 M LITHIUM SULFATE, AND 10 MM MAGNESIUM SULFATE IN 25 MM CITRATE BUFFER AT PH 6.0. THE PROTEIN SOLUTION CONTAINED 17 MG/ML R1 PROTEIN, 20-FOLD EXCESS FO A 20-RESIDUE PEPTIDE CORRESPONDING TO THE C-TERMINUS OF THE R2 SUBUNIT AND IS ESSENTIAL FOR CRYSTALLIZATION. 10 MM DTTP AND 10 MM GDP WAS ADDED TO THE PROTEIN SOLUTION 48 H BEFORE FREEZING THE PROTEIN CRYSTALS
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Uhlin, U., (1993) FEBS Lett., 336, 148.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 %lithium sulphate1reservoir
210 mMmagnesium sulphate1reservoir
325 mMsodium citrate1reservoirpH6.0
430 mg/mlprotein1drop
515 mg/mlpeptide solution1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→45 Å / Num. obs: 53514 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 2 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.308 / % possible all: 93.6
Reflection
*PLUS
Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 52.2 %

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Processing

Software
NameClassification
TNTrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementMethod to determine structure: RIGID BODY / Resolution: 3.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.308 -2 %RANDOM
obs0.278 65054 96.1 %-
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17925 0 174 0 18099
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_deg2.6

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