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- PDB-4m1f: X-ray crystal structure of E. coli apo NrdF -

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Basic information

Entry
Database: PDB / ID: 4m1f
TitleX-ray crystal structure of E. coli apo NrdF
ComponentsRibonucleoside-diphosphate reductase 2 subunit betaRibonucleotide reductase
KeywordsOXIDOREDUCTASE / ribonucleotide reductase
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / manganese ion binding
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / 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 ...Ribonucleoside-diphosphate reductase subunit beta / 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 2 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBoal, A.K. / Cotruvo Jr., J.A. / Stubbe, J. / Rosenzweig, A.C.
CitationJournal: To be Published
Title: X-ray crystal structure of E. coli apo NrdF
Authors: Boal, A.K. / Cotruvo Jr., J.A. / Stubbe, J. / Rosenzweig, A.C.
History
DepositionAug 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase 2 subunit beta


Theoretical massNumber of molelcules
Total (without water)36,4751
Polymers36,4751
Non-polymers00
Water4,288238
1
A: Ribonucleoside-diphosphate reductase 2 subunit beta

A: Ribonucleoside-diphosphate reductase 2 subunit beta


Theoretical massNumber of molelcules
Total (without water)72,9502
Polymers72,9502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area3610 Å2
ΔGint-18 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.511, 78.511, 267.294
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-606-

HOH

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Components

#1: Protein Ribonucleoside-diphosphate reductase 2 subunit beta / Ribonucleotide reductase / R2F protein / Ribonucleotide reductase 2


Mass: 36475.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2676, JW2651, nrdF, ygaD / Production host: Escherichia coli (E. coli)
References: UniProt: P37146, ribonucleoside-diphosphate reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG4000, 0.2 M sodium acetate, 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97897
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 23, 2010
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 2→29.987 Å / Num. all: 34048 / Num. obs: 33502 / % possible obs: 98.7 % / Redundancy: 10.6 % / Rsym value: 0.086 / Net I/σ(I): 25.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.673 / % possible all: 96.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N37

3n37


Resolution: 2→29.987 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.823 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1987 1704 5.1 %RANDOM
Rwork0.1762 ---
obs0.1774 33502 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.9 Å2 / Biso mean: 29.2023 Å2 / Biso min: 17.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.36 Å20 Å2
2--0.36 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2→29.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 0 238 2533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022361
X-RAY DIFFRACTIONr_bond_other_d0.0010.022271
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.963216
X-RAY DIFFRACTIONr_angle_other_deg0.7363.0015164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7725287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94724.821112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15515400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0741510
X-RAY DIFFRACTIONr_chiral_restr0.060.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02544
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 115 -
Rwork0.258 2253 -
all-2368 -
obs--96.89 %

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