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- PDB-4bmr: Crystal Structure of Ribonucleotide Reductase apo-NrdF from Bacil... -

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Basic information

Entry
Database: PDB / ID: 4bmr
TitleCrystal Structure of Ribonucleotide Reductase apo-NrdF from Bacillus cereus (space group P21)
ComponentsRIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT BETA
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / metal ion binding / membrane
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
: / Ribonucleoside-diphosphate reductase subunit beta
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHersleth, H.-P. / Tomter, A.B. / Hammerstad, M. / Rohr, A.K. / Andersson, K.K.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Crystal Structure of Bacillus Cereus Class Ib Ribonucleotide Reductase Di-Iron Nrdf in Complex with Nrdi.
Authors: Hammerstad, M. / Hersleth, H. / Tomter, A.B. / Rohr, A.K. / Andersson, K.K.
History
DepositionMay 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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 / struct_ncs_dom_lim / struct_site
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_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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 SUBUNIT BETA
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2184
Polymers74,1062
Non-polymers1122
Water2,612145
1
A: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1092
Polymers37,0531
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1092
Polymers37,0531
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.050, 53.850, 91.230
Angle α, β, γ (deg.)90.00, 110.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 286 / Label seq-ID: 1 - 286

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT BETA / RIBONUCLEOTIDE REDUCTASE NRDF


Mass: 37052.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q81G55, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 5.9 / Details: 0.2 M MG-FORMATE PH 5.9 AND 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2→34.25 Å / Num. obs: 35615 / % possible obs: 83.9 % / Observed criterion σ(I): 6 / Redundancy: 2.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.1 / % possible all: 83.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BMQ

4bmq


Resolution: 2→34.28 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.867 / SU B: 5.812 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25973 1800 5.1 %RANDOM
Rwork0.20832 ---
obs0.21087 33800 83.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.435 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-0.26 Å2
2---0.45 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 2→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4661 0 2 145 4808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194853
X-RAY DIFFRACTIONr_bond_other_d0.0050.024629
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9616573
X-RAY DIFFRACTIONr_angle_other_deg1.285310682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7375595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.27625.593236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.28615899
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1311515
X-RAY DIFFRACTIONr_chiral_restr0.1210.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025510
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021093
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1771.5222353
X-RAY DIFFRACTIONr_mcbond_other1.1761.5222352
X-RAY DIFFRACTIONr_mcangle_it1.8732.2752957
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6411.7372500
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 17134 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 148 -
Rwork0.32 2429 -
obs--83.16 %

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