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- PDB-3dhz: Apo (iron free) structure of C. ammoniagenes R2 protein -

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Basic information

Entry
Database: PDB / ID: 3dhz
TitleApo (iron free) structure of C. ammoniagenes R2 protein
ComponentsRibonucleotide reductase subunit R2F
KeywordsMETAL BINDING PROTEIN / metal free / ribonucleotide reductase / hydrogen bond
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
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 subunit beta
Similarity search - Component
Biological speciesCorynebacterium ammoniagenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsHogbom, M. / Nordlund, P.
CitationJournal: Biochemistry / Year: 2004
Title: Structural and mutational studies of the carboxylate cluster in Iron-free Ribonucleotide Reductase R2.
Authors: Andersson, M.E. / Hogbom, M. / Rinaldo-Matthis, A. / Blodig, W. / Liang, Y. / Persson, B.O. / Sjoberg, B.M. / Su, X.D. / Nordlund, P.
History
DepositionJun 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ribonucleotide reductase subunit R2F
B: Ribonucleotide reductase subunit R2F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1416
Polymers75,9182
Non-polymers2234
Water16,177898
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-41 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.908, 86.537, 70.610
Angle α, β, γ (deg.)90.00, 105.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonucleotide reductase subunit R2F


Mass: 37959.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium ammoniagenes (bacteria)
Gene: nrdF / Production host: Escherichia coli (E. coli) / References: UniProt: O69274
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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: 1.9 Å3/Da / Density % sol: 35.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% w/v PEG 4000, 100 mM sodium citrate, 200 mM Ammonium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.63→30 Å / Num. all: 67077 / Num. obs: 67077 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.63→1.69 Å / Rmerge(I) obs: 0.204 / % possible all: 86.6

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Processing

Software
NameClassification
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Model includes residual Fe ions at low occupancy
RfactorNum. reflectionSelection details
Rfree0.222 3358 random
Rwork0.165 --
all0.168 67038 -
obs0.168 67038 -
Refinement stepCycle: LAST / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 4 898 5734
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.76
X-RAY DIFFRACTIONc_bond_d0.018

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