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- PDB-1l1l: CRYSTAL STRUCTURE OF B-12 DEPENDENT (CLASS II) RIBONUCLEOTIDE RED... -

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Basic information

Entry
Database: PDB / ID: 1l1l
TitleCRYSTAL STRUCTURE OF B-12 DEPENDENT (CLASS II) RIBONUCLEOTIDE REDUCTASE
ComponentsRIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE
KeywordsOXIDOREDUCTASE / 10-stranded alpha-beta barrel / central finger loop
Function / homology
Function and homology information


ribonucleoside-triphosphate reductase (thioredoxin) / ribonucleoside-triphosphate reductase (thioredoxin) activity / cobalamin binding / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / DNA replication / nucleotide binding
Similarity search - Function
b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2 / b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2 / b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3 / b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3 / Ribonucleoside-triphosphate reductase, adenosylcobalamin-dependent / Ribonucleotide reductase, alpha helical domain / : / Ribonucleotide reductase alpha domain / B12-dependent ribonucleotide reductase, insertion domain / : ...b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2 / b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2 / b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3 / b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3 / Ribonucleoside-triphosphate reductase, adenosylcobalamin-dependent / Ribonucleotide reductase, alpha helical domain / : / Ribonucleotide reductase alpha domain / B12-dependent ribonucleotide reductase, insertion domain / : / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase, barrel domain / Alpha-Beta Barrel / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Adenosylcobalamin-dependent ribonucleoside-triphosphate reductase
Similarity search - Component
Biological speciesLactobacillus leichmannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsSintchak, M.D. / Arjara, G. / Kellogg, B.A. / Stubbe, J. / Drennan, C.L.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer.
Authors: Sintchak, M.D. / Arjara, G. / Kellogg, B.A. / Stubbe, J. / Drennan, C.L.
History
DepositionFeb 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Author states the sequence is correct and residue number 152 is PHE, there is an error in ...SEQUENCE Author states the sequence is correct and residue number 152 is PHE, there is an error in the reference database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE
B: RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE
C: RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE
D: RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)328,2844
Polymers328,2844
Non-polymers00
Water51,7932875
1
A: RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)82,0711
Polymers82,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)82,0711
Polymers82,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)82,0711
Polymers82,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)82,0711
Polymers82,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.500, 114.700, 121.300
Angle α, β, γ (deg.)90.00, 110.20, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is a monomer

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Components

#1: Protein
RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE


Mass: 82070.969 Da / Num. of mol.: 4 / Mutation: C731/736S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus leichmannii (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): JM105
References: UniProt: Q59490, ribonucleoside-triphosphate reductase (thioredoxin)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2875 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, PEG 8000, glycerol, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
250 mMsodium citrate1droppH5.6
320 %(v/v)glycerol1drop
41 mMdithiothreitol1drop
51 mMEDTA1drop
61.6 Mammonium sulfate1reservoir
72 %(v/w)PEG80001reservoir
820 %(v/v)glycerol1reservoir
9100 mMsodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1022 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jul 28, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1022 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 285688 / Num. obs: 285688 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rsym value: 0.058 / Net I/σ(I): 13.5
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.267 / % possible all: 60.2
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 632497 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 60.2 % / Rmerge(I) obs: 0.267

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 5512 RANDOM
Rwork0.223 --
all0.234 278508 -
obs-278508 -
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22352 0 0 2875 25227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.566
X-RAY DIFFRACTIONc_bond_d0.01
LS refinement shellResolution: 1.75→1.76 Å
RfactorNum. reflection% reflection
Rfree0.39 71 -
Rwork0.37 --
obs-2934 60 %
Refinement
*PLUS
Lowest resolution: 500 Å / Num. reflection obs: 272996 / Rfactor obs: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.57

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