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- PDB-1uzr: Crystal Structure of the Class Ib Ribonucleotide Reductase R2F-2 ... -

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Basic information

Entry
Database: PDB / ID: 1uzr
TitleCrystal Structure of the Class Ib Ribonucleotide Reductase R2F-2 subunit from Mycobacterium tuberculosis
ComponentsRIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT
KeywordsREDUCTASE / RIBONUCLEOTIDE REDUCTASE / TUBERCULOSIS / R2F-2 / RADICAL GENERATION / SMALL SUBUNIT
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / metal ion binding
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
CITRIC ACID / : / Ribonucleoside-diphosphate reductase subunit beta nrdF2 / Ribonucleoside-diphosphate reductase subunit beta nrdF2
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsUppsten, M. / Davis, J. / Rubin, H. / Uhlin, U.
CitationJournal: FEBS Lett. / Year: 2004
Title: Crystal Structure of the Biologically Active Form of Class Ib Ribonucleotide Reductase Small Subunit from Mycobacterium Tuberculosis
Authors: Uppsten, M. / Davis, J. / Rubin, H. / Uhlin, U.
History
DepositionMar 15, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / pdbx_struct_conn_angle / struct_conn
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 / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT
B: RIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT
C: RIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,71415
Polymers101,5263
Non-polymers1,18812
Water7,044391
1
A: RIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT
C: RIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,47610
Polymers67,6842
Non-polymers7928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT
hetero molecules

B: RIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,47610
Polymers67,6842
Non-polymers7928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)161.492, 161.492, 115.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.51235, 0.0328, 0.8514), (0.047, -0.9988, 0.0096), (0.857, 0.035, -0.5245)24.645, 51.2306, -46.7655
2given(0.4479, 0.0684, -0.8914), (0.0484, -0.9975, -0.0522), (-0.8927, -0.0198, -0.4501)53.3954, 107.0453, 93.7691

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Components

#1: Protein RIBONUCLEOTIDE REDUCTASE R2-2 SMALL SUBUNIT / RIBONUCLEOTIDE REDUCTASE / RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE R2-2 / BETA SUBUNIT


Mass: 33842.078 Da / Num. of mol.: 3 / Fragment: RADICAL GENERATING SUBUNIT, RESIDUES 1-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q50549, UniProt: P9WH71*PLUS, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 3.4 Å3/Da / Density % sol: 63.3 %
Crystal growpH: 5.6 / Details: 0.6 M AMSO4, 100MM NACT PH 5.6, 50MM NA/K TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 15, 2003
RadiationMonochromator: CRYOGENICALLY COOLED HIGH RESOLUTION SI (311) AND LOWER RESOLUTION SI (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 77125 / % possible obs: 99 % / Redundancy: 4.84 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.7 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R2F

1r2f


Resolution: 2.2→111.8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.876 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3870 5 %RANDOM
Rwork0.175 ---
obs0.177 73204 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.55 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→111.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6905 0 63 391 7359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0217107
X-RAY DIFFRACTIONr_bond_other_d0.0020.026353
X-RAY DIFFRACTIONr_angle_refined_deg1.851.969653
X-RAY DIFFRACTIONr_angle_other_deg0.973314746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.21069
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027884
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021482
X-RAY DIFFRACTIONr_nbd_refined0.2320.21651
X-RAY DIFFRACTIONr_nbd_other0.2340.27094
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0940.23966
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2356
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3550.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0131.54251
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.94726868
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.19132856
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.354.52785
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.25 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 274
Rwork0.279 5123

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