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- PDB-6tqy: Crystal structure of ribonucleotide reductase NrdF L61G variant f... -

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Basic information

Entry
Database: PDB / ID: 6tqy
TitleCrystal structure of ribonucleotide reductase NrdF L61G variant from Bacillus anthracis anaerobically soaked with Fe(II) and Mn(II) ions
ComponentsRibonucleoside-diphosphate reductase subunit beta
KeywordsOXIDOREDUCTASE / Metal binding / Oxidation reduction process / 2'-Deoxyribonucleotide metabolism / DNA replication
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / metal ion binding / membrane
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily ...Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ribonucleoside-diphosphate reductase subunit beta
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsGrave, K. / Hogbom, M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2020
Title: The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron.
Authors: Grave, K. / Griese, J.J. / Berggren, G. / Bennett, M.D. / Hogbom, M.
History
DepositionDec 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 3, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,70011
Polymers74,0002
Non-polymers7009
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-107 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.247, 60.495, 95.996
Angle α, β, γ (deg.)90.000, 106.525, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ribonucleoside-diphosphate reductase subunit beta


Mass: 36999.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: L61G variant / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: nrdF, GBAA_1372 / Variant: pXO1-/pXO2- deficient / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2
References: UniProt: Q81TB4, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8 - 2.0 M ammonium sulphate, 0.1 M Bis-Tris methane, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.76901830909→46.015 Å / Num. obs: 60567 / % possible obs: 98.2 % / Redundancy: 3.82 % / Biso Wilson estimate: 22.7525053055 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.063 / Χ2: 1.042 / Net I/σ(I): 13.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.77-1.883.6250.4322.6834760991295890.9110.50796.7
1.88-2.013.8490.2644.4535162930991350.9660.30798.1
2.01-2.1740.1637.3834373869185940.9860.18898.9
2.17-2.373.9320.10411.1431121799279150.9920.12199
2.37-2.653.6840.07114.9126233724371200.9960.08398.3
2.65-3.063.8090.05220.7624039641363110.9980.0698.4
3.06-3.743.9570.03630.4821301543453830.9990.04199.1
3.74-5.283.60.0334.9214830425241200.9980.03696.9
5.28-46.0153.980.02934.649553242824000.9990.03398.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QO9

6qo9


Resolution: 1.77→41.5580982367 Å / SU ML: 0.169587863033 / Cross valid method: FREE R-VALUE / σ(F): 1.35799330492 / Phase error: 21.5039447369
RfactorNum. reflection% reflectionSelection details
Rfree0.208969934425 3018 4.99321663744 %Random selection
Rwork0.168786321429 ---
obs0.170746993713 60442 98.0723673536 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.6597643133 Å2
Refinement stepCycle: LAST / Resolution: 1.77→41.5580982367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4635 0 29 278 4942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008200231381624776
X-RAY DIFFRACTIONf_angle_d0.9445152868686460
X-RAY DIFFRACTIONf_chiral_restr0.0485195187157713
X-RAY DIFFRACTIONf_plane_restr0.00576330187074819
X-RAY DIFFRACTIONf_dihedral_angle_d15.45563452651758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.79670.3240242676991300.252190038822472X-RAY DIFFRACTION92.895394502
1.7967-1.82610.2463073931351370.2240699772432602X-RAY DIFFRACTION98.3482944345
1.8261-1.85760.2447671538011370.2143978140382591X-RAY DIFFRACTION98.1648074847
1.8576-1.89140.2743135870211340.2071788631622561X-RAY DIFFRACTION95.9416162335
1.8914-1.92780.236661536211340.1995765486362565X-RAY DIFFRACTION97.6483357453
1.9278-1.96710.2481311603661370.1936712886282593X-RAY DIFFRACTION98.8056460369
1.9671-2.00990.2376746907751380.1815624328982622X-RAY DIFFRACTION98.9602007888
2.0099-2.05660.2522750257281390.1709201934512628X-RAY DIFFRACTION98.9274222381
2.0566-2.10810.1913787538871370.1751736435652598X-RAY DIFFRACTION98.6296429859
2.1081-2.16510.2185297534581370.1657148644752630X-RAY DIFFRACTION98.7508922198
2.1651-2.22880.209994137841380.1627621760262633X-RAY DIFFRACTION98.9642857143
2.2288-2.30070.2087408725061370.1549564289882611X-RAY DIFFRACTION98.9557075981
2.3007-2.38290.1919875657631390.1579193132512648X-RAY DIFFRACTION99.2874955468
2.3829-2.47830.1969540567051380.1590438042422615X-RAY DIFFRACTION98.92202659
2.4783-2.59110.1762331967131380.1615018916872617X-RAY DIFFRACTION98.2875490546
2.5911-2.72770.2167608098491340.1635943976052549X-RAY DIFFRACTION95.6506238859
2.7277-2.89850.222745244581390.1720733430912645X-RAY DIFFRACTION99.4640943194
2.8985-3.12230.1983286235751380.1791184667852650X-RAY DIFFRACTION99.5714285714
3.1223-3.43630.2126131215841410.1758033986212667X-RAY DIFFRACTION99.1175432404
3.4363-3.93320.1934625367841380.1500861308922627X-RAY DIFFRACTION98.7852804573
3.9332-4.95420.1807886429131390.1404241671332645X-RAY DIFFRACTION97.7871443625
4.9542-41.55809823670.2142068733671390.1823344533152655X-RAY DIFFRACTION95.914864401

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