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- PDB-1h78: STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION ... -

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Basic information

Entry
Database: PDB / ID: 1h78
TitleSTRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DCTP.
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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Anaerobic ribonucleoside-triphosphate reductase / Anaerobic ribonucleoside-triphosphate reductase
Similarity search - Component
Biological speciesBACTERIOPHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.0Jul 4, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.1Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_strain
Revision 2.2Dec 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 / 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 / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,0144
Polymers68,0561
Non-polymers9593
Water1,72996
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)138,0288
Polymers136,1112
Non-polymers1,9176
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)97.935, 97.935, 242.515
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-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 4.27 Å3/Da / Density % sol: 71.21 %
Crystal growpH: 7.5 / Details: PEG 400, MGCL2, HEPES, DTT, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0266
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 1999 / Details: BENT MIRROR
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0266 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 41517 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 52.6 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 21
Reflection shellResolution: 2.5→2.53 Å / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.3 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B8B.PDB

1b8b
PDB Unreleased entry


Resolution: 2.5→19.96 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: MLF TARGET FUNCTION RESIDUES 544-571 NOT MODELLED BUT HAVE WEAK DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3453 8.5 %RANDOM
Rwork0.221 ---
obs0.221 40833 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1816 Å2 / ksol: 0.345733 e/Å3
Displacement parametersBiso mean: 58.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.12 Å20 Å20 Å2
2--4.12 Å20 Å2
3----8.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4219 0 57 96 4372
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
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_deg2.1
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_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.021.5
X-RAY DIFFRACTIONc_mcangle_it3.182
X-RAY DIFFRACTIONc_scbond_it3.312
X-RAY DIFFRACTIONc_scangle_it4.482.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 579 8.8 %
Rwork0.3 6032 -
obs--96.7 %

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