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- PDB-4xbv: R2-like ligand-binding oxidase with anaerobically reconstituted d... -

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Basic information

Entry
Database: PDB / ID: 4xbv
TitleR2-like ligand-binding oxidase with anaerobically reconstituted diiron cofactor
ComponentsRibonuleotide reductase small subunit
KeywordsOXIDOREDUCTASE / R2-like ligand-binding oxidase / diiron cofactor / ribonucleotide reductase R2 subunit fold / metalloprotein
Function / homology
Function and homology information


deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
R2-like ligand binding oxidase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PALMITIC ACID / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsGriese, J.J. / Hogbom, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor.
Authors: Griese, J.J. / Kositzki, R. / Schrapers, P. / Branca, R.M. / Nordstrom, A. / Lehtio, J. / Haumann, M. / Hogbom, M.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuleotide reductase small subunit
B: Ribonuleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,77410
Polymers73,9262
Non-polymers8488
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-92 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.584, 98.077, 55.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribonuleotide reductase small subunit / R2-LIKE LIGAND-BINDING OXIDASE


Mass: 36962.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria)
Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-FE2 / FE (II) ION


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


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 27.5% (w/v) PEG 1500, 0.1 M HEPES-Na, pH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2013
RadiationMonochromator: Si(111) monochromator and Rh mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. obs: 66383 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 29.08 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.35
Reflection shellResolution: 1.799→1.91 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 1.75 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1606)refinement
XDSdata reduction
Cootmodel building
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HR4

4hr4


Resolution: 1.799→48.622 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 3316 5 %random selection
Rwork0.1885 ---
obs0.1905 66349 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.7 Å2
Refinement stepCycle: LAST / Resolution: 1.799→48.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 42 218 4983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184907
X-RAY DIFFRACTIONf_angle_d1.2866577
X-RAY DIFFRACTIONf_dihedral_angle_d14.7061815
X-RAY DIFFRACTIONf_chiral_restr0.055687
X-RAY DIFFRACTIONf_plane_restr0.007847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7986-1.82430.42331260.3682423X-RAY DIFFRACTION94
1.8243-1.85150.41231380.36882619X-RAY DIFFRACTION100
1.8515-1.88040.34591370.34782596X-RAY DIFFRACTION100
1.8804-1.91130.34381360.32712584X-RAY DIFFRACTION100
1.9113-1.94420.34711380.31082621X-RAY DIFFRACTION100
1.9442-1.97960.32381360.29142579X-RAY DIFFRACTION100
1.9796-2.01760.31481370.27422606X-RAY DIFFRACTION100
2.0176-2.05880.27141370.23782607X-RAY DIFFRACTION100
2.0588-2.10360.25321370.23192592X-RAY DIFFRACTION100
2.1036-2.15250.25961380.21992632X-RAY DIFFRACTION100
2.1525-2.20640.21491360.18892590X-RAY DIFFRACTION100
2.2064-2.2660.2541390.17932628X-RAY DIFFRACTION100
2.266-2.33270.20671380.17272627X-RAY DIFFRACTION100
2.3327-2.4080.21931380.17162618X-RAY DIFFRACTION100
2.408-2.49410.19781370.17312612X-RAY DIFFRACTION100
2.4941-2.59390.22691390.16642631X-RAY DIFFRACTION100
2.5939-2.71190.21871390.17792637X-RAY DIFFRACTION100
2.7119-2.85490.1881380.17182636X-RAY DIFFRACTION100
2.8549-3.03380.22731390.17712640X-RAY DIFFRACTION100
3.0338-3.26790.21991400.18752662X-RAY DIFFRACTION100
3.2679-3.59670.20561410.17292670X-RAY DIFFRACTION100
3.5967-4.11690.21171410.15342681X-RAY DIFFRACTION100
4.1169-5.1860.20261430.14882721X-RAY DIFFRACTION100
5.186-48.64020.21721480.19142821X-RAY DIFFRACTION99

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