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- PDB-4col: Crystal structure of the anaerobic ribonucleotide reductase from ... -

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Basic information

Entry
Database: PDB / ID: 4col
TitleCrystal structure of the anaerobic ribonucleotide reductase from Thermotoga maritima with dATP bound in the specificity site
ComponentsANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE
KeywordsOXIDOREDUCTASE / RADICAL CHEMISTRY / ALLOSTERIC REGULATION / ANAEROBIC ENZYME
Function / homology
Function and homology information


anaerobic ribonucleoside-triphosphate reductase complex / ribonucleoside-triphosphate reductase (thioredoxin) activity / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / DNA replication / nucleotide binding / metal ion binding
Similarity search - Function
Ribonucleoside-triphosphate reductase, anaerobic / Anaerobic ribonucleoside-triphosphate reductase
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / SULFONIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsAurelius, O. / Johansson, R. / Bagenholm, V. / Beck, T. / Balhuizen, A. / Lundin, D. / Sjoberg, B.M. / Mulliez, E. / Logan, D.T.
CitationJournal: Plos One / Year: 2015
Title: The Crystal Structure of Thermotoga Maritima Class III Ribonucleotide Reductase Lacks a Radical Cysteine Pre-Positioned in the Active Site.
Authors: Aurelius, O. / Johansson, R. / Bagenholm, V. / Beck, T. / Balhuizen, A. / Lundin, D. / Sjoberg, B.M. / Mulliez, E. / Logan, D.T.
History
DepositionJan 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 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 / struct_site
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 / _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: ANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE
B: ANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,67710
Polymers151,3492
Non-polymers1,3288
Water6,377354
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-64.8 kcal/mol
Surface area40310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.000, 94.120, 86.710
Angle α, β, γ (deg.)90.00, 112.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6762, -0.01091, -0.7366), (-0.01732, -0.9998, -0.001091), (-0.7365, 0.0135, -0.6763)
Vector: 22.73, 7.524, 51.74)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE / ANAEROBIC RIBONUCLEOTIDE REDUCTASE


Mass: 75674.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL
References: UniProt: Q9WYL6, ribonucleoside-triphosphate reductase (thioredoxin)

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Non-polymers , 5 types, 362 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-SFO / SULFONIC ACID


Mass: 83.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3O3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 1.95 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growDetails: A NATIVE CRYSTAL (20 MG/ML, 12% [W/V] PEG3000, 100 MM MES PH 5.9, 5 MM DTT) SOAKED WITH 0.5 MM DATP, 10 MM MGCL2 AND 20% (V/V) PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 18, 2013
Details: TOROIDAL MIRROR FOR HORIZONTAL AND VERTICAL FOCUSING
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→29.1 Å / Num. obs: 82717 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 24.92 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 1.96→2.08 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4COI

4coi


Resolution: 1.96→29.136 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 2078 2.5 %
Rwork0.1911 --
obs0.192 82656 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→29.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9639 0 72 354 10065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069953
X-RAY DIFFRACTIONf_angle_d1.02713448
X-RAY DIFFRACTIONf_dihedral_angle_d14.7963674
X-RAY DIFFRACTIONf_chiral_restr0.0611433
X-RAY DIFFRACTIONf_plane_restr0.0051694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9602-2.00580.31291540.28175264X-RAY DIFFRACTION98
2.0058-2.05590.25191110.24335402X-RAY DIFFRACTION100
2.0559-2.11150.28731610.23185347X-RAY DIFFRACTION100
2.1115-2.17360.2591140.2245402X-RAY DIFFRACTION100
2.1736-2.24370.43491310.345217X-RAY DIFFRACTION96
2.2437-2.32390.39791320.34955164X-RAY DIFFRACTION96
2.3239-2.41690.2261370.20295396X-RAY DIFFRACTION100
2.4169-2.52680.25581420.1835425X-RAY DIFFRACTION100
2.5268-2.660.2021300.17245360X-RAY DIFFRACTION100
2.66-2.82650.2091470.17845396X-RAY DIFFRACTION100
2.8265-3.04450.22471540.18555401X-RAY DIFFRACTION100
3.0445-3.35050.2281250.18675431X-RAY DIFFRACTION100
3.3505-3.83440.23151460.17115398X-RAY DIFFRACTION100
3.8344-4.82730.15121510.14045453X-RAY DIFFRACTION100
4.8273-29.13950.1761430.1585522X-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)
12.6273-0.33021.33170.5971-0.16133.5194-0.00370.4990.0219-0.0517-0.1011-0.0853-0.21470.56380.08750.2073-0.0728-0.00060.30680.04490.233113.16877.073436.2198
22.92210.08040.90511.82430.23993.61130.1034-0.6198-0.09140.1944-0.02710.11950.0927-0.8566-0.07080.2093-0.06820.00270.52130.06020.2224-5.34871.270855.2679
32.9869-0.58061.41760.6343-0.39414.49850.083-0.0781-0.11620.0882-0.0496-0.09370.21580.5912-0.01540.2236-0.0368-0.02390.3162-0.01080.215521.96760.377254.8316
43.27791.1151.41942.16751.38332.82520.52080.1522-0.94210.15030.1587-0.31821.145-0.2372-0.65470.5525-0.1529-0.14220.36160.06610.46991.4393-15.359347.3449
51.6022-0.18670.09240.45310.00782.78490.0420.87740.0482-0.1427-0.1281-0.3367-0.1421.5270.06150.30690.12490.02861.1850.02170.360320.02144.047212.7657
62.678-0.11011.1320.771-0.46223.99910.0684-0.2069-0.2298-0.07290.05830.06920.5345-0.1455-0.08060.2482-0.0256-0.03010.1741-0.03190.2139-7.2379-2.727421.6894
72.5088-0.150.91811.5121-0.43384.29-0.0224-0.6938-0.059-0.06460.02440.1781-0.0187-1.0091-0.01470.19240.0422-0.03240.4943-0.01120.2654-21.13255.575321.0198
83.7543-0.44630.87860.78010.28094.3691-0.04110.2062-0.0945-0.07490.01720.14190.1915-0.08440.03370.2776-0.0012-0.0580.2073-0.01460.1763-12.51975.22975.276
92.75680.20751.57061.4293-0.37034.2711-0.04250.960.0195-0.25280.0175-0.04560.25031.02860.03110.30390.02340.00170.5849-0.03140.21821.32973.0588-2.0819
105.67370.043-1.0070.0628-0.55793.5163-0.13980.47091.1818-0.1045-0.0540.0439-1.03080.18390.14870.5218-0.0605-0.12860.30820.10510.4088-9.019316.9237-2.4328
110.9259-0.21710.08241.32560.67193.2437-0.429-0.34910.5273-0.12410.1092-0.0912-0.9923-0.20670.29990.45840.1477-0.14830.3309-0.09520.4562-13.741921.708615.3272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 197 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 198 THROUGH 351 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 352 THROUGH 579 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 580 THROUGH 630 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 1 THROUGH 94 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 95 THROUGH 197 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 198 THROUGH 298 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 299 THROUGH 386 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 387 THROUGH 517 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 518 THROUGH 566 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 567 THROUGH 632 )

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