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- PDB-3o0o: Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3o0o
TitleThermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP, GDP and Adenosylcobalamin
ComponentsRibonucleoside-diphosphate reductaseRibonucleotide reductase
KeywordsOXIDOREDUCTASE / 10 alpha/beta barrel / adenosylcobalamin dependent / ribonucleotide reductase / Reduction ribonucleotide 2'-OH position / EFFECTOR / DTTP / SUBSTRATE / GDP / COENZYME B12
Function / homology
Function and homology information


cobalamin binding / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA biosynthetic process / DNA replication / ATP binding
Similarity search - Function
Ribonucleotide reductase, adenosylcobalamin-dependent / 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 / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / GUANOSINE-5'-DIPHOSPHATE / THYMIDINE-5'-TRIPHOSPHATE / Vitamin B12-dependent ribonucleotide reductase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement / Resolution: 1.9 Å
AuthorsLarsson, K.-M. / Logan, D.T. / Nordlund, P.
CitationJournal: Acs Chem.Biol. / Year: 2010
Title: Structural Basis for Adenosylcobalamin Activation in AdoCbl-Dependent Ribonucleotide Reductases.
Authors: Larsson, K.M. / Logan, D.T. / Nordlund, P.
History
DepositionJul 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2012Group: Non-polymer description
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Ribonucleoside-diphosphate reductase
B: Ribonucleoside-diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,81112
Polymers146,7482
Non-polymers5,06310
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-62 kcal/mol
Surface area45590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.020, 124.230, 107.170
Angle α, β, γ (deg.)90.00, 102.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ribonucleoside-diphosphate reductase / Ribonucleotide reductase


Mass: 73374.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: nrdJ, TM_0118 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O33839, ribonucleoside-diphosphate reductase

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Non-polymers , 6 types, 473 molecules

#2: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#6: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSTUDIES SUGGEST A POINT MUTATION EITHER IN THE SEQUENCING CLONE (SER->TYR MUTATION) OR IN THEIR ...STUDIES SUGGEST A POINT MUTATION EITHER IN THE SEQUENCING CLONE (SER->TYR MUTATION) OR IN THEIR EXPRESSION CLONE (TYR->SER). CODONS FOR TYR=ATA AND SER=AGA.

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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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% PEG8000, 0.1M sodium acetate, 0.1 M sodium chloride, 10mM DTT (dithiotreithol), 5% glycerol, crystallization geometry: 4 microL protein 11miligram/milliL + 2uL reservoir solution over ...Details: 10% PEG8000, 0.1M sodium acetate, 0.1 M sodium chloride, 10mM DTT (dithiotreithol), 5% glycerol, crystallization geometry: 4 microL protein 11miligram/milliL + 2uL reservoir solution over 300 microL in 24-well plate. Crystals in 3-4 days, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979162 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979162 Å / Relative weight: 1
ReflectionResolution: 1.9→49 Å / Num. all: 120492 / Num. obs: 119789 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.42 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.064
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 1.6 / Num. unique all: 17143 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.2_432)refinement
REFMACrefinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: Rigid body refinement
Starting model: PDB entry 1XJE

1xje


Resolution: 1.9→46.937 Å / SU ML: 0.32 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 5993 5 %
Rwork0.2022 --
obs0.204 119774 99.45 %
all-120492 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.177 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.6805 Å2-0 Å28.1781 Å2
2---1.9529 Å20 Å2
3----8.7276 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9874 0 334 463 10671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810558
X-RAY DIFFRACTIONf_angle_d1.13914368
X-RAY DIFFRACTIONf_dihedral_angle_d16.8434132
X-RAY DIFFRACTIONf_chiral_restr0.0731587
X-RAY DIFFRACTIONf_plane_restr0.0051800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.4265830.406911397X-RAY DIFFRACTION100
1.9679-2.04670.37935810.345511380X-RAY DIFFRACTION100
2.0467-2.13990.34455670.311367X-RAY DIFFRACTION99
2.1399-2.25270.32195910.264811355X-RAY DIFFRACTION99
2.2527-2.39380.30215820.246511312X-RAY DIFFRACTION99
2.3938-2.57860.26236240.21311289X-RAY DIFFRACTION99
2.5786-2.83810.25996390.204611294X-RAY DIFFRACTION99
2.8381-3.24870.25596190.193211392X-RAY DIFFRACTION100
3.2487-4.09260.19725640.169311496X-RAY DIFFRACTION100
4.0926-46.95160.17746430.154311499X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5649-0.6451-1.28240.681-0.78163.1419-0.4106-1.2069-0.60760.0497-0.01720.1596-0.10280.74840.36650.49170.2091-0.04971.07930.40940.3455-84.0271-76.118311.8972
22.0566-0.4427-1.26851.03820.19382.13770.2422-1.23670.0126-0.11540.0206-0.1376-0.22560.9222-0.23940.1773-0.24780.0140.9434-0.03860.1704-86.8314-51.79237.3248
30.9523-1.1-0.13231.8996-0.29540.4116-0.1469-0.0943-0.3964-0.07560.00060.61440.2060.16720.17891.03170.02710.10250.89240.08621.0337-103.599-78.58638.7118
41.9133-0.5391-0.83210.3510.0240.89160.151-1.3752-0.42880.25750.02730.1702-0.17740.2861-0.14470.1825-0.2132-0.07630.89870.26020.3157-108.8964-59.429615.0264
50.69560.477-0.12460.6563-0.01330.3930.2028-0.07050.48730.0367-0.0520.243-0.58050.0135-0.14360.5211-0.07960.09360.1732-0.00620.345-80.0329-28.9154-47.6353
60.66770.1881-0.27741.78130.04661.7117-0.0572-0.0598-0.04330.04880.0449-0.00450.09350.22570.01270.19670.03520.04770.14220.0110.1834-76.2874-51.3269-42.2869
71.24530.8413-0.22060.926-0.51990.46090.35210.11090.6470.2265-0.13430.6983-0.2256-0.0642-0.21830.3950.03650.02880.32140.14280.682-102.6791-42.7854-62.6863
80.5613-0.2609-0.12510.2241-0.04730.8711-0.18450.0861-0.2746-0.22510.09090.14470.41980.01720.02720.3145-0.0448-0.01960.1397-0.01530.3099-89.9835-61.0482-56.4771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:40)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 41:511)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 512:528)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 529:633)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 1:66)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 67:511)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 512:551)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 552:633)

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