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- PDB-1yfd: Crystal structure of the Y122H mutant of ribonucleotide reductase... -

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Basic information

Entry
Database: PDB / ID: 1yfd
TitleCrystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. coli
ComponentsRibonucleoside-diphosphate reductase 1 beta chain
KeywordsOXIDOREDUCTASE / di-iron 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, 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
MU-OXO-DIIRON / : / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKolberg, M. / Logan, D.T. / Bleifuss, G. / Poetsch, S. / Sjoeberg, B.M. / Graeslund, A. / Lubitz, W. / Lassmann, G. / Lendzian, F.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies
Authors: Kolberg, M. / Logan, D.T. / Bleifuss, G. / Poetsch, S. / Sjoeberg, B.M. / Graeslund, A. / Lubitz, W. / Lassmann, G. / Lendzian, F.
History
DepositionDec 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 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)89,66717
Polymers86,8042
Non-polymers2,86315
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-389 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.040, 84.740, 115.030
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: 43401.836 Da / Num. of mol.: 2 / Mutation: Y122H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: Expression system used in combination with a second plasmid, pGP1-2, for overexpression of R2-Y122H using heat induction of the T7 RNA polymerase
Gene: nrdB, ftsB / Plasmid: pTB2-Y122H / Production host: Escherichia coli (E. coli) / Strain (production host): MC1009
References: UniProt: P69924, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, 0.1M MES, 0.4M NACL, 1mM EMTS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 27, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.9→19.6 Å / Num. obs: 57178 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.084 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 6.8 / Rsym value: 0.233 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
MAR345data collection
XDSdata scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PFR

1pfr


Resolution: 1.9→19.46 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.493 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.132 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STEREOCHEMICAL DISTORTIONS reported in remark 500 ARE DUE TO THE PROXIMITY OF THESE RESIDUES TO STRONGLY DIFFRACTING MERCURY IONS IN THE CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.20601 2312 4 %RANDOM
Rwork0.17314 ---
obs0.17449 54865 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.662 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2--0.31 Å20 Å2
3---0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.132 Å0.148 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5578 0 19 438 6035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225706
X-RAY DIFFRACTIONr_bond_other_d0.0010.025100
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9337740
X-RAY DIFFRACTIONr_angle_other_deg0.897311874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1435679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33924.521292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.547151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2781534
X-RAY DIFFRACTIONr_chiral_restr0.0840.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021169
X-RAY DIFFRACTIONr_nbd_refined0.2270.21399
X-RAY DIFFRACTIONr_nbd_other0.1780.25243
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.23134
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2359
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2570.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9971.54456
X-RAY DIFFRACTIONr_mcbond_other0.1751.51366
X-RAY DIFFRACTIONr_mcangle_it1.15325530
X-RAY DIFFRACTIONr_scbond_it1.9932709
X-RAY DIFFRACTIONr_scangle_it2.8234.52210
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.379 155
Rwork0.337 3897

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