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- PDB-1r1r: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN MUTANT Y730F WITH A REDUCED A... -

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Basic information

Entry
Database: PDB / ID: 1r1r
TitleRIBONUCLEOTIDE REDUCTASE R1 PROTEIN MUTANT Y730F WITH A REDUCED ACTIVE SITE FROM ESCHERICHIA COLI
Components
  • RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
  • RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
KeywordsOXIDOREDUCTASE / DEOXYRIBONUCLEOTIDE SYNTHESIS / RADICAL CHEMISTRY / REDOX CENTER / RIBONUCLEOTIDE REDUCTASE
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: 2.9 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: J.Biol.Chem. / Year: 1996
Title: Two Conserved Tyrosine Residues in Protein R1 Participate in an Intermolecular Electron Transfer in Ribonucleotide Reductase
Authors: Ekberg, M. / Sahlin, M. / Eriksson, M. / Sjoberg, B.M.
#2: Journal: Nature / Year: 1994
Title: Structure of Ribonucleotide Reductase Protein R1
Authors: Uhlin, U. / Eklund, H.
History
DepositionJul 15, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 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


Theoretical massNumber of molelcules
Total (without water)266,6697
Polymers266,6697
Non-polymers00
Water5,621312
1
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
P: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)90,4043
Polymers90,4043
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)88,1322
Polymers88,1322
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-14 kcal/mol
Surface area29470 Å2
MethodPISA
3
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)88,1322
Polymers88,1322
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-14 kcal/mol
Surface area29490 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)528,79512
Polymers528,79512
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 area26630 Å2
ΔGint-147 kcal/mol
Surface area160360 Å2
MethodPISA
5
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
x 6


Theoretical massNumber of molelcules
Total (without water)528,79512
Polymers528,79512
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 area26170 Å2
ΔGint-149 kcal/mol
Surface area161000 Å2
MethodPISA
6
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)515,1676
Polymers515,1676
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 area13550 Å2
ΔGint-69 kcal/mol
Surface area160540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.820, 227.820, 343.470
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(-0.9034, 0.4288, 0.0005), (0.4288, 0.9034, 0.0003), (-0.0003, 0.0004, -1)-56.4547, 12.632, -7.8039
2given(-0.729, 0.685, -0.007), (-0.685, -0.729, 0.001), (-0.005, 0.006, 1)-89.859, 95.812, 3.208

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Components

#1: Protein RIBONUCLEOTIDE REDUCTASE R1 PROTEIN


Mass: 85861.086 Da / Num. of mol.: 3 / Mutation: Y730F
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.: 312 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45 %
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
*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: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: SEGMENTAL TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 77589 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 15.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.338 / % possible all: 95
Reflection shell
*PLUS
% possible obs: 52.2 % / Rmerge(I) obs: 0.373

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Processing

Software
NameClassification
TNTrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementMethod to determine structure: RIGID BODY / Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2265 3 %RANDOM
Rwork0.21 ---
obs0.22 75509 96.1 %-
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17950 0 0 312 18262
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_deg1.7

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