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- PDB-1pm2: CRYSTAL STRUCTURE OF MANGANESE SUBSTITUTED R2-D84E (D84E MUTANT O... -

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Basic information

Entry
Database: PDB / ID: 1pm2
TitleCRYSTAL STRUCTURE OF MANGANESE SUBSTITUTED R2-D84E (D84E MUTANT OF THE R2 SUBUNIT OF E. COLI RIBONUCLEOTIDE REDUCTASE)
ComponentsRibonucleoside-diphosphate reductase 1 beta chain
KeywordsOXIDOREDUCTASE / four-helix bundle / diiron center
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
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 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVoegtli, W.C. / Sommerhalter, M. / Baldwin, J. / Saleh, L. / Bollinger Jr., J.M. / Rosenzweig, A.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Variable coordination geometries at the diiron(II) active site of ribonucleotide reductase R2.
Authors: Voegtli, W.C. / Sommerhalter, M. / Saleh, L. / Baldwin, J. / Bollinger Jr., J.M. / Rosenzweig, A.C.
History
DepositionJun 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase 1 beta chain
B: Ribonucleoside-diphosphate reductase 1 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,03820
Polymers79,0102
Non-polymers3,02818
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-363 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.95, 83.94, 114.34
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonucleoside-diphosphate reductase 1 beta chain / Ribonucleotide reductase 1 / B2 protein / R2 protein


Mass: 39504.754 Da / Num. of mol.: 2 / Mutation: D84E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RIR2 / Production host: Escherichia coli (E. coli)
References: UniProt: P69924, 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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.25 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 4000, MES, sodium chloride, sodium ethylmercurithiosalicylicate , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMHEPES1droppH7.6
31 mMEMTS1drop
450 mMMES1reservoirpH6.0
520 %(w/v)PEG40001reservoir
6200 mM1reservoirNaCl
71 mMEMTS1reservoir
80.5 %(w/v)dioxane1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 278856 / Num. obs: 278856 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.06 / Net I/σ(I): 8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 3.5 / Num. unique all: 9590 / Rsym value: 0.206 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 66524 / Num. measured all: 566232 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PIZ

1piz


Resolution: 1.8→25 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 6725 -random
Rwork0.185 ---
all0.185 66394 --
obs0.185 66394 99.7 %-
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-2.853 Å20 Å20 Å2
2---2.491 Å20 Å2
3----0.362 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 18 439 6013
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shellResolution: 1.8→1.9 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection% reflection
Rfree0.255 1116 -
Rwork0.236 --
obs-10904 99.8 %
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1

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