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Basic information

Entry
Database: PDB / ID: 4com
TitleCrystal structure of the anaerobic ribonucleotide reductase from Thermotoga maritima with MES 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 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 / MOLECULAR REPLACEMENT / Resolution: 1.92 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 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _diffrn_source.pdbx_synchrotron_site
Revision 2.1Dec 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_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)152,1087
Polymers151,3492
Non-polymers7605
Water12,827712
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9570 Å2
ΔGint-35.2 kcal/mol
Surface area44980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.590, 96.030, 89.600
Angle α, β, γ (deg.)90.00, 112.66, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6612, 0.02988, -0.7496), (0.02513, -0.9995, -0.01767), (-0.7498, -0.00715, -0.6616)
Vector: 16.41, -7.185, 36.08)

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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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.12 Å3/Da / Density % sol: 41.9 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.0097
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2011
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: 1.0097 Å / Relative weight: 1
ReflectionResolution: 1.89→29.4 Å / Num. obs: 100224 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 28.02 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8
Reflection shellResolution: 1.89→2 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.2 / % possible all: 94.5

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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 ETRY 4COI

4coi


Resolution: 1.92→29.399 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 2410 2.5 %
Rwork0.1535 --
obs0.1542 95838 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→29.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9781 0 42 712 10535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0210166
X-RAY DIFFRACTIONf_angle_d1.47713735
X-RAY DIFFRACTIONf_dihedral_angle_d14.193802
X-RAY DIFFRACTIONf_chiral_restr0.0911455
X-RAY DIFFRACTIONf_plane_restr0.0061744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.95920.28261500.22895496X-RAY DIFFRACTION99
1.9592-2.00180.23131370.21125446X-RAY DIFFRACTION100
2.0018-2.04830.25371510.19665465X-RAY DIFFRACTION100
2.0483-2.09950.23311310.17885494X-RAY DIFFRACTION100
2.0995-2.15630.21971520.17075481X-RAY DIFFRACTION100
2.1563-2.21970.19171320.16285464X-RAY DIFFRACTION100
2.2197-2.29130.20291360.16055517X-RAY DIFFRACTION100
2.2913-2.37320.21091220.16065521X-RAY DIFFRACTION100
2.3732-2.46820.17441440.15445446X-RAY DIFFRACTION100
2.4682-2.58040.17391440.15345495X-RAY DIFFRACTION100
2.5804-2.71640.16881390.14885518X-RAY DIFFRACTION100
2.7164-2.88650.20331450.15485502X-RAY DIFFRACTION100
2.8865-3.10910.20431580.15945482X-RAY DIFFRACTION100
3.1091-3.42150.19191290.15695512X-RAY DIFFRACTION100
3.4215-3.91570.17821460.14185542X-RAY DIFFRACTION100
3.9157-4.92960.13841520.12355519X-RAY DIFFRACTION100
4.9296-29.40270.16081420.15335528X-RAY DIFFRACTION98
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)
11.3009-0.25320.2621.1254-0.55012.9162-0.0857-0.1789-0.03810.18120.05470.2127-0.0848-0.40950.00080.17240.01310.03410.264-0.01530.20865.4719-3.160331.3224
21.39220.0718-0.40490.6035-0.04271.4708-0.02150.0936-0.05120.14280.0097-0.1755-0.01430.20470.00620.16620.0061-0.04390.19450.01790.226141.3801-4.254122.8988
30.8699-0.11820.14791.76541.18971.8791-0.0307-0.23110.04520.29480.0577-0.0764-0.0827-0.0446-0.02710.33840.0207-0.00750.20880.01980.173524.9529-0.766344.9366
41.52470.6819-0.46661.9193-2.12082.74480.00640.03920.56860.3970.14410.0618-0.5746-0.0899-0.08640.4642-0.0032-0.03180.2485-0.01790.446339.054314.650931.5941
51.940.03090.1140.45690.07780.7837-0.0193-0.0680.03920.02730.02260.0631-0.0067-0.1475-0.01430.1580.0314-0.00130.2101-0.02110.19453.0885-1.53688.8232
61.9830.1634-0.07931.42230.37011.1504-0.06660.2926-0.0497-0.23180.146-0.2154-0.08760.30880.01350.1784-0.01850.04450.3365-0.02590.190533.3952-1.9287-8.0574
71.6260.643-1.70362.08681.01963.3511-0.07260.6261-0.0421-0.61870.1711-0.0739-0.0324-0.01120.02190.3137-0.05250.0520.4879-0.0550.236123.666-8.6085-20.2653
81.76510.47130.26641.06320.31741.203-0.10680.4173-0.0997-0.20960.08970.04250.0584-0.06660.02410.20610.0014-0.01880.3404-0.00070.1882-0.4033-6.1708-12.1816
91.25750.67620.33341.006-1.2553.3021-0.07650.5386-0.6148-0.54260.1773-0.21620.60190.1423-0.00920.4641-0.07450.0470.5854-0.18110.338216.9445-17.4254-22.7069
105.8113-1.18254.21797.7372-5.54795.99910.2974-0.4137-0.70850.11360.04010.6390.0512-0.1653-0.2840.4250.05220.03650.44-0.0850.492422.6541-26.7484-3.8611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 118 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 119 THROUGH 386 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 387 THROUGH 546 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 547 THROUGH 632 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 1 THROUGH 151 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 152 THROUGH 276 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 277 THROUGH 351 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 352 THROUGH 546 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 547 THROUGH 593 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 594 THROUGH 630 )

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