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- PDB-2alx: Ribonucleotide Reductase R2 from Escherichia coli in space group ... -

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Basic information

Entry
Database: PDB / ID: 2alx
TitleRibonucleotide Reductase R2 from Escherichia coli in space group P6(1)22
ComponentsRibonucleoside-diphosphate reductase 1Ribonucleotide reductase
KeywordsOXIDOREDUCTASE / ribonucleotide reductase R2 / new crystal form / diiron center / dimanganese 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 / cytosol / cytoplasm
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / 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: 2.6 Å
AuthorsSommerhalter, M. / Saleh, L. / Bollinger Jr., J.M. / Rosenzweig, A.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Escherichia coli ribonucleotide reductase R2 in space group P6122.
Authors: Sommerhalter, M. / Saleh, L. / Bollinger, J.M. / Rosenzweig, A.C.
History
DepositionAug 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Aug 23, 2023Group: 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 / 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5487
Polymers39,6361
Non-polymers9126
Water0
1
A: Ribonucleoside-diphosphate reductase 1
hetero molecules

A: Ribonucleoside-diphosphate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,09614
Polymers79,2722
Non-polymers1,82412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7310 Å2
ΔGint-229 kcal/mol
Surface area23330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.940, 92.940, 200.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer, generated from the monomer in the asymmetric unit by the operation -y, -x, -z+5/6 (crystallographic symmetry operation 6 in space group P6(1)22.

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Components

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


Mass: 39635.945 Da / Num. of mol.: 1 / Fragment: residues 0-339
Source method: isolated from a genetically manipulated source
Details: beta subunit, R2 subunit / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nrdB, ftsB / 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.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg

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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: 2.89 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, MES, manganese chloride, magnesium chloride, 4-(2-Hydroxyethyl)-1-piperazinepropanesulfonic acid, ethylmercurithiosalicylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→19.27 Å / Num. all: 16493 / Num. obs: 16493 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 6.1
Reflection shellResolution: 2.6→2.74 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 1.9 / Num. measured obs: 2353 / Rsym value: 0.383 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ENTRY ID 1PIY, Chain A

1piy


Resolution: 2.6→19.27 Å / Isotropic thermal model: group / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1647 10 %random
Rwork0.227 ---
all0.232 16469 --
obs0.232 16437 99.8 %-
Solvent computationBsol: 58.353 Å2
Displacement parametersBiso mean: 61.126 Å2
Baniso -1Baniso -2Baniso -3
1--10.796 Å2-13.515 Å20 Å2
2---10.796 Å20 Å2
3---21.591 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 6 0 2788
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.183
X-RAY DIFFRACTIONc_dihedral_angle_d19.18
X-RAY DIFFRACTIONc_improper_angle_d0.856
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.384 242 -
Rwork0.323 --
obs-2418 100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2topper_ion.param

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