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- PDB-1hk8: STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION ... -

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Basic information

Entry
Database: PDB / ID: 1hk8
TitleSTRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DGTP
ComponentsANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE
KeywordsOXIDOREDUCTASE / REDUCTASE / ALLOSTERIC REGULATION / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


ribonucleoside-triphosphate reductase (formate) / ribonucleoside-triphosphate reductase activity / 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 / 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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / : / Anaerobic ribonucleoside-triphosphate reductase
Similarity search - Component
Biological speciesBACTERIOPHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLarsson, K.-M. / Andersson, J. / Sjoeberg, B.-M. / Nordlund, P. / Logan, D.T.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: A Metal-Binding Site in the Catalytic Subunit of Anaerobic Ribonucleotide Reductase.
Authors: Logan, D.T. / Mulliez, E. / Larsson, K.-M. / Bodevin, S. / Atta, M. / Garnaud, P.E. / Sjoberg, B.-M. / Fontecave, M.
#1: Journal: Structure / Year: 2001
Title: Structural basis for allosteric substrate specificity regulation in anaerobic ribonucleotide reductases.
Authors: Larsson, K.M. / Andersson, J. / Sjoberg, B.M. / Nordlund, P. / Logan, D.T.
History
DepositionMar 6, 2003Deposition site: PDBE / Processing site: PDBE
SupersessionMar 27, 2003ID: 1H77
Revision 1.0Mar 27, 2003Provider: 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 1.4Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1905
Polymers68,0561
Non-polymers1,1354
Water4,107228
1
A: ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE
hetero molecules

A: ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,38110
Polymers136,1112
Non-polymers2,2698
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)98.163, 98.163, 246.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

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Components

#1: Protein ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE 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\: P.YOUNG, M.OHMAN, M.Q.XU. / Source: (gene. exp.) BACTERIOPHAGE T4 (virus) / Plasmid: PET29T4NRDD(G580A) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3)
References: UniProt: P07071, ribonucleoside-triphosphate reductase (thioredoxin)
#2: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY INVOLVES 2'-DEOXYRIBONUCLEOSIDE TRIPHOSPHATE + OXIDIZED THIOREDOXIN + H(2)O = ...CATALYTIC ACTIVITY INVOLVES 2'-DEOXYRIBONUCLEOSIDE TRIPHOSPHATE + OXIDIZED THIOREDOXIN + H(2)O = RIBONUCLEOSIDE TRIPHOSPHATE + REDUCED THIOREDOXIN. ENGINEERED MUTATION GLY 580 ALA

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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: 4.5 Å3/Da / Density % sol: 72.4 %
Crystal growpH: 7.5 / Details: 30% PEG 400, 02M MGCL2, 0.1M HEPES PH 7.5, 7MM DTT
Crystal grow
*PLUS
Method: unknown / Details: Logan, D.T., (1999) Science, 283, 1499.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.043
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1999 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.043 Å / Relative weight: 1
ReflectionResolution: 2.43→37.8 Å / Num. obs: 44361 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.3
Reflection shellResolution: 2.43→2.49 Å / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3.8 / % possible all: 94.1
Reflection
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 20 Å / % possible obs: 95 % / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B8B

1b8b
PDB Unreleased entry


Resolution: 2.45→20.08 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.546 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1742 4.2 %RANDOM
Rwork0.204 ---
obs-39943 95.7 %-
Displacement parametersBiso mean: 41.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4411 0 64 228 4703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214575
X-RAY DIFFRACTIONr_bond_other_d0.0020.024047
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9646209
X-RAY DIFFRACTIONr_angle_other_deg0.81839458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025050
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02915
X-RAY DIFFRACTIONr_nbd_refined0.1860.2975
X-RAY DIFFRACTIONr_nbd_other0.2190.24777
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0150.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.98322788
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.17334514
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.04821787
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.13631695
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.52 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 116
Rwork0.275 2298
Software
*PLUS
Name: REFMAC / Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS

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