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- PDB-1h7b: Structural basis for allosteric substrate specificity regulation ... -

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Basic information

Entry
Database: PDB / ID: 1h7b
TitleStructural basis for allosteric substrate specificity regulation in class III ribonucleotide reductases, native NRDD
ComponentsANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN
KeywordsOXIDOREDUCTASE / REDUCTASE / ALLOSTERIC REGULATION / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


ribonucleoside-triphosphate reductase (formate) / ribonucleoside-triphosphate reductase (thioredoxin) activity / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / DNA replication / metal ion binding
Similarity search - Function
Ribonucleoside-triphosphate reductase, anaerobic / Anaerobic ribonucleoside-triphosphate reductase / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Glycine radical domain / Glycine radical domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Anaerobic ribonucleoside-triphosphate reductase / Anaerobic ribonucleoside-triphosphate reductase
Similarity search - Component
Biological speciesBACTERIOPHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.45 Å
AuthorsLarsson, K.-M. / Andersson, J. / Sjoeberg, B.-M. / Nordlund, P. / Logan, D.T.
CitationJournal: Structure / Year: 2001
Title: Structural Basis for Allosteric Substrate Specificty Regulation in Anaerobic Ribonucleotide Reductase
Authors: Larsson, K.-M. / Andersson, J. / Sjoeberg, B.-M. / Nordlund, P. / Logan, D.T.
History
DepositionJul 4, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1512
Polymers68,0561
Non-polymers951
Water1,982110
1
A: ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN
hetero molecules

A: ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,3014
Polymers136,1112
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)98.019, 98.019, 242.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN / ANAEROBIC NTP REDUCTASE


Mass: 68055.594 Da / Num. of mol.: 1 / Fragment: ACTIVE SITE SUBUNIT, RESIDUES 1-605 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SEQUENCE DETERMINATION. YOUNG, P., OHMAN, M., XU, M.Q.
Source: (gene. exp.) BACTERIOPHAGE T4 (virus) / Plasmid: PET29T4NRDD(G580A) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3)
References: UniProt: Q9T0V5, UniProt: P07071*PLUS, ribonucleoside-triphosphate reductase (thioredoxin)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 4.28 Å3/Da / Density % sol: 71.25 %
Crystal growpH: 7.5
Details: 30% PEG 400, 0.2M MGCL2, 0.1M HEPES PH 7.5, 7MM DTT
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Logan, D.T., (1999) Science, 283, 1499.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MHEPES-NaOH1reservoirpH7.5
20.2 M1reservoirMgCl2
35-7 mMdithiothreitol1reservoir
426-32 %PEG4001reservoir
520-30 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.028
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2000 / Details: BENT MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.028 Å / Relative weight: 1
ReflectionResolution: 2.42→20 Å / Num. obs: 43746 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 24.3
Reflection shellResolution: 2.42→2.46 Å / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 4 / % possible all: 96.4
Reflection
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 20 Å / % possible obs: 95 % / Redundancy: 4.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.45→19.87 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1842807.9 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD FUNCTION ON F
Details: THE REGIONS BETWEEN RESIDUES 544 AND 571, ARE INCOMPLETELY REFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3548 8.4 %RANDOM
Rwork0.224 ---
obs0.224 42011 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.763 Å2 / ksol: 0.404686 e/Å3
Displacement parametersBiso mean: 57.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.66 Å20 Å20 Å2
2--4.66 Å20 Å2
3----9.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.45→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4213 0 5 110 4328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.44→2.59 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 579 8.8 %
Rwork0.293 5981 -
obs--89.5 %
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.229 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09

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