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

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Basic information

Entry
Database: PDB / ID: 4con
TitleCrystal structure of the anaerobic ribonucleotide reductase from Thermotoga maritima with citrate in the active 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 / DNA replication / nucleotide binding / metal ion binding
Similarity search - Function
Ribonucleoside-triphosphate reductase, anaerobic / Anaerobic ribonucleoside-triphosphate reductase
Similarity search - Domain/homology
CITRIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 1.2Dec 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 / 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 / _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)151,7334
Polymers151,3492
Non-polymers3842
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-41.6 kcal/mol
Surface area40400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.550, 97.740, 86.580
Angle α, β, γ (deg.)90.00, 112.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6582, -0.07659, -0.7489), (-0.07549, -0.9965, 0.03557), (-0.7491, 0.03313, -0.6617)
Vector: 24.09, 7.569, 52.5)

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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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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 Å3/Da / Density % sol: 39.6 % / Description: NONE
Crystal growDetails: 24 MG/ML, 13% (W/V) PEG3000, 100 MM CITRATE PH 5.3 AND 5 MM DTT. SOAKED IN 20% (V/V) PEG400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2010 / Details: ONE PAIR OF PT COATED SI MIRROR
RadiationMonochromator: HORIZONTALLY SIDE DIFFRACTING SI(111) CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.12→42.58 Å / Num. obs: 68379 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8
Reflection shellResolution: 2.12→2.25 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.1 / % possible all: 98

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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: 2.12→41.733 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 1712 2.5 %
Rwork0.1822 --
obs0.1831 68347 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→41.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8996 0 26 188 9210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099246
X-RAY DIFFRACTIONf_angle_d1.09312480
X-RAY DIFFRACTIONf_dihedral_angle_d14.623414
X-RAY DIFFRACTIONf_chiral_restr0.0811331
X-RAY DIFFRACTIONf_plane_restr0.0051583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1204-2.18280.3491370.29385418X-RAY DIFFRACTION97
2.1828-2.25320.35191380.29565548X-RAY DIFFRACTION100
2.2532-2.33380.33471290.26035546X-RAY DIFFRACTION100
2.3338-2.42720.29171540.23335552X-RAY DIFFRACTION100
2.4272-2.53760.20091400.21615577X-RAY DIFFRACTION100
2.5376-2.67140.22551360.19875533X-RAY DIFFRACTION100
2.6714-2.83870.24421460.20155565X-RAY DIFFRACTION100
2.8387-3.05790.26491650.20595574X-RAY DIFFRACTION100
3.0579-3.36550.24011260.19335585X-RAY DIFFRACTION100
3.3655-3.85220.18731490.16995566X-RAY DIFFRACTION100
3.8522-4.85220.17731480.13615583X-RAY DIFFRACTION99
4.8522-41.74080.17671440.14775588X-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)
12.5234-0.80471.12670.5611-0.07041.95370.1030.63760.0634-0.1247-0.1939-0.2096-0.11720.87850.07640.3016-0.03840.02540.76610.08680.352628.89243.076830.6588
22.34710.1721-0.13570.4376-0.54882.1117-0.0281-0.70950.05290.09810.01460.1337-0.3665-1.9656-0.02470.28180.05260.06951.7529-0.13030.4169-3.64366.84151.2423
32.6969-1.42221.91462.3116-0.74624.6863-0.02-0.2386-0.02260.2241-0.1101-0.0183-0.05420.06350.11950.2206-0.1189-0.01080.41760.00130.254126.16182.349252.2272
46.30071.1811-2.89241.8913-1.22241.6165-0.1807-0.9651-0.86260.1934-0.07960.12390.6035-0.59740.20510.5119-0.25090.02990.92840.08410.457912.4068-6.538465.6779
52.91320.1970.93291.0261-0.56283.40210.0491-0.16350.0283-0.1076-0.1141-0.07330.25730.32380.04380.27940.04370.00620.2849-0.04770.26014.19782.225919.4287
62.0452-0.17970.58840.714-0.34274.12240.0422-0.06410.077-0.1650.02830.11390.1657-0.3041-0.05210.3402-0.0343-0.03080.1792-0.07060.2727-7.24514.4555.6426
76.3984-0.0277-0.77950.3221-0.85473.8086-0.0437-0.0231.0198-0.13370.13030.1588-0.6314-0.4187-0.09610.50120.0365-0.02880.3087-0.03080.4323-11.72816.7113-0.9022
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 352 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 353 THROUGH 535 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 536 THROUGH 588 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 1 THROUGH 216 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 217 THROUGH 517 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 518 THROUGH 589 )

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