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

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Basic information

Entry
Database: PDB / ID: 4coj
TitleCrystal structure of the anaerobic ribonucleotide reductase from Thermotoga maritima in complex with dATP and CTP
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 / DNA replication / nucleotide binding / metal ion binding
Similarity search - Function
Ribonucleoside-triphosphate reductase, anaerobic / Anaerobic ribonucleoside-triphosphate reductase
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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 28, 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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)153,47710
Polymers151,3492
Non-polymers2,1288
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-79 kcal/mol
Surface area40980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.983, 94.509, 87.068
Angle α, β, γ (deg.)90.00, 112.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6726, -0.001583, -0.74), (-0.00181, -1, 0.000495), (-0.74, 0.001007, -0.6726)
Vector: 22.89, 7.603, 51.8)

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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, 189 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 1.97 Å3/Da / Density % sol: 37.5 % / Description: NONE
Crystal growDetails: A NATIVE CRYSTAL (20 MG/ML, 16% [W/V] PEG3000, 100 MM MES PH 6.1, 5 MM DTT) SOAKED WITH 0.5 MM DATP, 2 MM CTP, 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: 0.98
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2013
Details: TOROIDAL MIRROR FOR HORIZONTAL AND VERTICAL FOCUSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.42→29.4 Å / Num. obs: 44053 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 2.42→2.56 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→29.14 Å / SU ML: 0.33 / σ(F): 1.71 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 1050 2.5 %
Rwork0.2036 --
obs0.2047 41467 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 2.48→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9783 0 122 181 10086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610170
X-RAY DIFFRACTIONf_angle_d0.78613724
X-RAY DIFFRACTIONf_dihedral_angle_d14.1213767
X-RAY DIFFRACTIONf_chiral_restr0.031455
X-RAY DIFFRACTIONf_plane_restr0.0031722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4801-2.61070.31951550.28455752X-RAY DIFFRACTION100
2.6107-2.77420.33721270.27885758X-RAY DIFFRACTION99
2.7742-2.98820.29681680.25965760X-RAY DIFFRACTION100
2.9882-3.28850.32931370.23425765X-RAY DIFFRACTION100
3.2885-3.76350.26961610.21025731X-RAY DIFFRACTION99
3.7635-4.73840.17881420.1565788X-RAY DIFFRACTION99
4.7384-29.14210.16791600.15495863X-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)
11.3144-0.54490.16960.5838-0.13121.7945-0.04880.4882-0.0454-0.185-0.1525-0.0225-0.41330.85580.07030.1112-0.0910.08650.95370.07270.239117.00916.607634.5137
21.55160.2284-0.36790.66830.1521.82150.1854-0.5653-0.12660.4392-0.003-0.04840.0087-1.38970.07970.04-0.12370.09621.09670.07040.2391-7.77981.856354.2715
31.28230.31940.13791.5156-0.67892.2527-0.1144-0.32870.31320.20640.020.0362-0.42461.10770.10510.317-0.1208-0.03510.55380.03050.259922.35068.82352.3604
42.433-0.73490.86071.1978-0.52662.79640.0942-0.1593-0.22760.1522-0.1439-0.03090.22610.66820.04530.2855-0.0098-0.02540.53550.04180.206222.1623-1.963155.7618
51.57631.24870.30112.56361.30471.79950.2864-0.237-0.46830.07890.0811-0.15341.0322-0.2655-0.21180.6146-0.162-0.13570.38490.17580.48333.7942-14.662252.2967
61.67420.15720.6620.7865-0.58282.11890.11990.4789-0.1272-0.1488-0.1225-0.19190.24870.9544-0.01510.23640.04460.05670.68760.00640.23548.94051.155816.0939
71.55780.37170.39961.6072-0.03831.52680.0617-0.6174-0.1021-0.24430.02970.25450.0058-1.3354-0.0560.1513-0.0327-0.04650.92340.01170.2994-22.3555.079120.1639
81.86230.17410.79520.9502-0.38932.9692-0.00910.67060.1007-0.191-0.0546-0.06210.14870.78510.05310.3262-0.01960.00090.5250.00360.2006-0.79645.9756-1.9126
90.8764-0.06710.33882.12971.83723.0899-0.42-0.36590.5585-0.24560.2296-0.2033-0.8392-0.15080.17310.49190.1066-0.1420.3865-0.07690.4192-12.778621.073811.5458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 178 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 179 THROUGH 320 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 321 THROUGH 417 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 418 THROUGH 566 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 567 THROUGH 633 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 1 THROUGH 178 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 179 THROUGH 350 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 351 THROUGH 546 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 547 THROUGH 637 )

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