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

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Basic information

Entry
Database: PDB / ID: 4coi
TitleCrystal structure of the anaerobic ribonucleotide reductase from Thermotoga maritima with glycerol in the active site
ComponentsANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE
KeywordsOXIDOREDUCTASE / RADICAL CHEMISTRY / ALLOSTERIC REGULATION / ANAEROBIC ENZYME
Function / homologyanaerobic ribonucleoside-triphosphate reductase complex / Ribonucleoside-triphosphate reductase, anaerobic / Anaerobic ribonucleoside-triphosphate reductase / ribonucleoside-triphosphate reductase (thioredoxin) activity / 2'-deoxyribonucleotide biosynthetic process / DNA replication / nucleotide binding / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 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 1.0Jan 14, 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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)151,9409
Polymers151,3492
Non-polymers5917
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-49.1 kcal/mol
Surface area42840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.890, 98.820, 86.980
Angle α, β, γ (deg.)90.00, 112.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6689, -0.02149, -0.7431), (-0.01683, -0.9998, 0.01377), (-0.7432, 0.003291, -0.6691)
Vector: 23.4, 7.507, 52.3)

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Components

#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)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.05 Å3/Da / Density % sol: 39.9 % / Description: NONE
Crystal growpH: 5.3
Details: 24 MG/ML, 8% (W/V) PEG3000, 0.1 M CITRATE BUFFER PH 5.3, 5 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0391
DetectorType: MARRESEARCH MARMOSAIC 165 / Detector: CCD / Date: Oct 26, 2010 / Details: VERTICALLY FOCUSING MULTILAYER MIRROR
RadiationMonochromator: BENT SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0391 Å / Relative weight: 1
ReflectionResolution: 1.94→24.3 Å / Num. obs: 87892 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 27.81 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.1 / % possible all: 91.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.94→24.303 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 2210 2.5 %
Rwork0.1814 --
obs0.1823 87864 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→24.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9967 0 32 469 10468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610272
X-RAY DIFFRACTIONf_angle_d0.99513861
X-RAY DIFFRACTIONf_dihedral_angle_d13.873815
X-RAY DIFFRACTIONf_chiral_restr0.0591472
X-RAY DIFFRACTIONf_plane_restr0.0041759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9402-1.98240.36671300.33784825X-RAY DIFFRACTION88
1.9824-2.02850.29721370.28415264X-RAY DIFFRACTION97
2.0285-2.07920.26541350.2435329X-RAY DIFFRACTION97
2.0792-2.13540.27151390.22455330X-RAY DIFFRACTION98
2.1354-2.19820.25851340.21075350X-RAY DIFFRACTION98
2.1982-2.26910.24531250.19985366X-RAY DIFFRACTION98
2.2691-2.35010.25751330.19725403X-RAY DIFFRACTION98
2.3501-2.44410.22671440.18085347X-RAY DIFFRACTION98
2.4441-2.55530.2541390.18195398X-RAY DIFFRACTION99
2.5553-2.68980.22231280.17685405X-RAY DIFFRACTION98
2.6898-2.85810.22031430.17485414X-RAY DIFFRACTION99
2.8581-3.07840.23311570.17935399X-RAY DIFFRACTION99
3.0784-3.38740.19231260.17215433X-RAY DIFFRACTION99
3.3874-3.87590.211480.15955433X-RAY DIFFRACTION99
3.8759-4.87670.18161460.15045458X-RAY DIFFRACTION99
4.8767-24.30450.17571460.17135500X-RAY DIFFRACTION99
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)
11.7608-0.11260.14430.2866-0.06770.96990.03260.18220.0759-0.0311-0.0051-0.0201-0.0410.0453-0.03460.1678-0.00990.00210.11430.02270.153118.61796.468934.072
22.1709-0.4001-0.22151.06940.20582.0865-0.0237-0.461-0.15610.04780.03760.1455-0.0072-0.3232-0.03030.13150.00610.02770.29980.05170.1778-7.06232.428653.4898
32.6526-0.0939-0.07530.80590.16181.0755-0.051-0.60940.02630.15260.06170.0489-0.150.031-0.03420.2096-0.0035-0.00190.21970.01620.133815.19674.457655.6397
41.5446-0.56310.42981.3861-0.43681.20930.002-0.204-0.06430.16660.0115-0.0256-0.02120.0759-0.00850.1821-0.0206-0.010.14740.0060.159225.97450.91753.4133
52.11531.14350.661.97271.70612.12120.0441-0.1489-0.66830.06430.0999-0.16980.22780.0926-0.06790.30220.02170.01190.22880.11770.4037.6754-13.943353.0583
61.15980.60170.55920.76380.19152.4853-0.0940.2850.0175-0.02630.0721-0.0952-0.050.53550.01230.18590.02620.0210.29070.02730.201919.06115.726211.5376
71.6699-0.05260.16320.2629-0.08562.1667-0.0345-0.1287-0.0881-0.08890.07860.13850.0732-0.3214-0.02910.1733-0.025-0.02320.12170.0090.1992-15.01013.254218.6956
80.9284-0.29560.6481.1027-0.76632.0279-0.10480.28010.0298-0.1460.0545-0.045-0.06050.18850.04530.2483-0.0630.00250.2038-0.01350.15820.72376.9885-2.7494
91.55770.19840.03681.90390.92532.4618-0.1395-0.05360.5585-0.24850.122-0.0708-0.60290.05420.01390.38440.0208-0.02960.17480.00310.3873-9.753422.479211.9569
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 310 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 311 THROUGH 386 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 387 THROUGH 546 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 547 THROUGH 639 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 1 THROUGH 118 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 119 THROUGH 386 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 387 THROUGH 550 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 551 THROUGH 640 )

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