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- PDB-5r1r: RIBONUCLEOTIDE REDUCTASE E441A MUTANT R1 PROTEIN FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 5r1r
TitleRIBONUCLEOTIDE REDUCTASE E441A MUTANT R1 PROTEIN 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 / cytoplasm / cytosol
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 / RIGID BODY / Resolution: 3.1 Å
AuthorsEriksson, M. / Eklund, H.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase.
Authors: Persson, A.L. / Eriksson, M. / Katterle, B. / Potsch, S. / Sahlin, M. / Sjoberg, B.M.
#1: 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.
#2: Journal: Nature / Year: 1994
Title: Structure of Ribonucleotide Reductase Protein R1
Authors: Uhlin, U. / Eklund, H.
History
DepositionSep 17, 1997Processing site: BNL
Revision 1.0Mar 18, 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)266,5437
Polymers266,5437
Non-polymers00
Water1,62190
1
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
P: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)90,3623
Polymers90,3623
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)88,0902
Polymers88,0902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-14 kcal/mol
Surface area28750 Å2
MethodPISA
3
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)88,0902
Polymers88,0902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-14 kcal/mol
Surface area28720 Å2
MethodPISA
4
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

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

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


Theoretical massNumber of molelcules
Total (without water)528,54312
Polymers528,54312
Non-polymers00
Water1086
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 area28860 Å2
ΔGint-177 kcal/mol
Surface area154580 Å2
MethodPISA
5
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
x 6


Theoretical massNumber of molelcules
Total (without water)528,54312
Polymers528,54312
Non-polymers00
Water1086
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 area28740 Å2
ΔGint-177 kcal/mol
Surface area154600 Å2
MethodPISA
6
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)264,2716
Polymers264,2716
Non-polymers00
Water543
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 area10730 Å2
ΔGint-74 kcal/mol
Surface area81000 Å2
MethodPISA
7
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)264,2716
Polymers264,2716
Non-polymers00
Water543
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 area10630 Å2
ΔGint-72 kcal/mol
Surface area81080 Å2
MethodPISA
8
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

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

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


Theoretical massNumber of molelcules
Total (without water)264,2716
Polymers264,2716
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10590 Å2
ΔGint-73 kcal/mol
Surface area81070 Å2
MethodPISA
9
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)514,9146
Polymers514,9146
Non-polymers00
Water1086
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 area15200 Å2
ΔGint-87 kcal/mol
Surface area154580 Å2
MethodPISA
10
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
E: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)176,1814
Polymers176,1814
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-39 kcal/mol
Surface area55010 Å2
MethodPISA
11
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

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


Theoretical massNumber of molelcules
Total (without water)176,1814
Polymers176,1814
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area6150 Å2
ΔGint-39 kcal/mol
Surface area54960 Å2
MethodPISA
12
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)88,0902
Polymers88,0902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-14 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.810, 223.810, 334.260
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(-0.902159, 0.431394, 0.002933), (0.431403, 0.902141, 0.005709), (-0.000183, 0.006416, -0.999979)-55.9091, 12.4334, -6.602
2given(-0.731638, 0.681681, -0.004058), (-0.681662, -0.731648, -0.005263), (-0.006557, -0.001084, 0.999978)-88.0775, 94.5832, 3.0105

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Components

#1: Protein RIBONUCLEOTIDE REDUCTASE R1 PROTEIN


Mass: 85819.055 Da / Num. of mol.: 3 / Mutation: E441A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.02 Å3/Da / Density % sol: 56 %
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 OF 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 OF A 20-RESIDUE PEPTIDE CORRESPONDING TO THE C-TERMINUS OF THE R2 SUBUNIT AND IS ESSENTIAL FOR CRYSTALLIZATION
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 mg/mlprotein1drop
217 %lithium sulfate1reservoir
310 mMmagnesium sulfate1reservoir
425 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Type: NSLS / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 53031 / % possible obs: 90.9 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 13.2
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.29 / % possible all: 89.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
REFMACrefinement
TNTphasing
RefinementMethod to determine structure: RIGID BODY
Starting model: PDB ENTRY 1RLR

1rlr


Resolution: 3.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 -2 %RANDOM
Rwork0.196 ---
obs0.199 52838 90.9 %-
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18533 0 0 90 18623
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 52838
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d2.4

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