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- PDB-6sf5: Mn-containing form of the ribonucleotide reductase NrdB protein f... -

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Basic information

Entry
Database: PDB / ID: 6sf5
TitleMn-containing form of the ribonucleotide reductase NrdB protein from Leeuwenhoekiella blandensis
ComponentsRibonucleoside-diphosphate reductase, beta subunit 1
KeywordsMETAL BINDING PROTEIN / ribonucleotide reductase apoprotein manganese binding redox protein deoxyribonucleotide synthesis
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesLeeuwenhoekiella blandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHasan, M. / Rozman Grinberg, I. / Sjoberg, B.M. / Logan, D.T.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-04855 Sweden
Swedish Research Council2016-01920 Sweden
Wenner-Gren Foundation Sweden
CitationJournal: J.Biol.Inorg.Chem. / Year: 2019
Title: Class Id ribonucleotide reductase utilizes a Mn2(IV,III) cofactor and undergoes large conformational changes on metal loading.
Authors: Rozman Grinberg, I. / Berglund, S. / Hasan, M. / Lundin, D. / Ho, F.M. / Magnuson, A. / Logan, D.T. / Sjoberg, B.M. / Berggren, G.
History
DepositionAug 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
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, beta subunit 1
B: Ribonucleoside-diphosphate reductase, beta subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3766
Polymers81,1562
Non-polymers2204
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-36 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.06, 80.602, 158.228
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonucleoside-diphosphate reductase, beta subunit 1


Mass: 40577.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leeuwenhoekiella blandensis (bacteria) / Gene: MED217_17135 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): /pET28a(+)
References: UniProt: A3XHF9, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein at 7.5 mg/ml in 50 mM Tris-HCl pH 7.8, 300 mM NaCl, 10% glycerol, 20 mM MgCl2, 2 mM tris(2-carboxyethyl)phosphine (TCEP) and 10 mM MnCl2. 200+200 nl sitting drops. Precipitant 0.1 M ...Details: Protein at 7.5 mg/ml in 50 mM Tris-HCl pH 7.8, 300 mM NaCl, 10% glycerol, 20 mM MgCl2, 2 mM tris(2-carboxyethyl)phosphine (TCEP) and 10 mM MnCl2. 200+200 nl sitting drops. Precipitant 0.1 M Bis-Tris pH 5.5, 25% w/v polyethylene glycol 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→80.6 Å / Num. obs: 17348 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.028 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 1.137 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3670 / CC1/2: 0.475 / Rpim(I) all: 0.658 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SF4

6sf4


Resolution: 1.9→71.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2895 -RANDOM
Rwork0.175 ---
obs0.176 58284 99.9 %-
Displacement parametersBiso mean: 51.11 Å2
Baniso -1Baniso -2Baniso -3
1--13.5696 Å20 Å20 Å2
2--7.562 Å20 Å2
3---6.0076 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.9→71.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4893 0 4 387 5284
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015042HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.946818HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1816SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes866HARMONIC5
X-RAY DIFFRACTIONt_it5042HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion17.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion659SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6364SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.91 Å
RfactorNum. reflection% reflection
Rfree0.3088 51 -
Rwork0.2221 1115 -
all0.2257 1166 -
obs--98.37 %
Refinement TLS params.

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)
11.0701-0.71460.50722.04310.151.79060.0246-0.1438-0.116-0.14380.00730.0343-0.1160.0343-0.0319-0.1329-0.02880.0345-0.1074-0.0085-0.078827.3507-1.922155.943
21.41170.88490.59232.07360.8542.30580.17140.52490.07160.5249-0.176-0.42390.0716-0.42390.0046-0.00080.02440.0742-0.08720.0118-0.195920.09918.4655189.872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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