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- PDB-3r1r: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH AMPPNP OCCUPYING THE ACT... -

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Basic information

Entry
Database: PDB / ID: 3r1r
TitleRIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH AMPPNP OCCUPYING THE ACTIVITY SITE 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 / DNA replication / iron ion 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 / DNA replication / 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
ADENOSINE-5'-TRIPHOSPHATE / Ribonucleoside-diphosphate reductase 1 subunit alpha / Ribonucleoside-diphosphate reductase 1 subunit beta / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY / Resolution: 3 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 21, 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)268,23810
Polymers266,7177
Non-polymers1,5223
Water1,51384
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)90,9274
Polymers90,4203
Non-polymers5071
Water181
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)88,6563
Polymers88,1482
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-11 kcal/mol
Surface area28610 Å2
MethodPISA
3
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6563
Polymers88,1482
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-12 kcal/mol
Surface area28600 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)538,74821
Polymers535,70515
Non-polymers3,0436
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 area31300 Å2
ΔGint-149 kcal/mol
Surface area154520 Å2
MethodPISA
5
C: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
F: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)531,93418
Polymers528,89112
Non-polymers3,0436
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 area29750 Å2
ΔGint-141 kcal/mol
Surface area154140 Å2
MethodPISA
6
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)531,93418
Polymers528,89112
Non-polymers3,0436
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 area29900 Å2
ΔGint-141 kcal/mol
Surface area154060 Å2
MethodPISA
7
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
P: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)525,12015
Polymers522,0779
Non-polymers3,0436
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 area21120 Å2
ΔGint-89 kcal/mol
Surface area154590 Å2
MethodPISA
8
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
hetero molecules

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
hetero molecules

A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
B: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)518,30612
Polymers515,2636
Non-polymers3,0436
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 area19730 Å2
ΔGint-81 kcal/mol
Surface area154130 Å2
MethodPISA
9
A: RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
D: RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6563
Polymers88,1482
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-12 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.610, 224.610, 336.630
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(-0.9047, 0.4261, 0.0018), (0.4261, 0.9047, 0.005), (0.0006, 0.0053, -1)-55.3473, 12.1865, -6.9446
2given(-0.7283, 0.6852, -0.008), (-0.6853, -0.7283, -0.0053), (-0.0094, 0.0016, 1)-88.6163, 94.5218, 2.9461

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Components

#1: Protein RIBONUCLEOTIDE REDUCTASE R1 PROTEIN


Mass: 85877.086 Da / Num. of mol.: 3
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
References: UniProt: P00453, UniProt: P69924*PLUS
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.15 Å3/Da / Density % sol: 43 %
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 AMPPNP AND 10 MM CDP WAS ALSO INCLUDED IN THE PROTEIN SOLUTION
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: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.95
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: #1 COLLIMATING TOROID,#2 BENT CYLINDER
RadiationMonochromator: DOUBLE FLAT CRYSTAL FIXED-EXIT MONOCHROMATOR USING SI(111) FLATS
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 68245 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 10.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.35 / % possible all: 83.8
Reflection
*PLUS
% possible obs: 96.1 %
Reflection shell
*PLUS
% possible obs: 42.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
REFMACrefinement
TNTphasing
RefinementMethod to determine structure: RIGID BODY / Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 -5 %RANDOM
obs0.263 65054 96.1 %-
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17921 0 93 84 18098
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_deg3

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