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- PDB-4do2: Crystal Structure of the Rop protein mutant D30P/A31G at resoluti... -

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Basic information

Entry
Database: PDB / ID: 4do2
TitleCrystal Structure of the Rop protein mutant D30P/A31G at resolution 1.4 resolution.
ComponentsRegulatory protein rop
KeywordsRNA BINDING PROTEIN / protein structure / protein folding / Rop protein / bacterial protein / mutation / 4-alpha-helical bundle / loop / ColE1 plasmid copy number
Function / homologyHelix Hairpins - #230 / Regulatory protein Rop / Rop-like superfamily / Rop protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsAmprazi, M. / Kapetaniou, E.G. / Kokkinidis, M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural plasticity of 4-alpha-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein.
Authors: Amprazi, M. / Kotsifaki, D. / Providaki, M. / Kapetaniou, E.G. / Fellas, G. / Kyriazidis, I. / Perez, J. / Kokkinidis, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Purification, crystallization and preliminary X-ray diffraction analysis of a variant of the ColE1 Rop protein.
Authors: Ambrazi, M. / Fellas, G. / Kapetaniou, E.G. / Kotsifaki, D. / Providaki, M. / Kokkinidis, M.
History
DepositionFeb 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references / Structure summary
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein rop
B: Regulatory protein rop


Theoretical massNumber of molelcules
Total (without water)16,3262
Polymers16,3262
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-27 kcal/mol
Surface area6390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.669, 38.823, 56.644
Angle α, β, γ (deg.)90.000, 100.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Regulatory protein rop / RNA one modulator / ROM


Mass: 8163.035 Da / Num. of mol.: 2 / Mutation: D30P, A31G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rop / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03051
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.8 Å3/Da / Density % sol: 31.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 45%(v/v) methanol, 50 mM HEPES pH 6.4 and 100 mM Li2SO4, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.817 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 20, 2006 / Details: mirrors
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.817 Å / Relative weight: 1
ReflectionResolution: 1.4→55.7 Å / Num. all: 22394 / Num. obs: 22394 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.4→1.45 Å / % possible all: 97.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ROP

1rop


Resolution: 1.401→55.64 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 0.964 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1877 1142 5.1 %RANDOM
Rwork0.1587 ---
obs0.1602 22275 98.96 %-
all-22275 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.36 Å2 / Biso mean: 17.6643 Å2 / Biso min: 7.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å2-0.16 Å2
2--0.42 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.401→55.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 0 169 1079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021943
X-RAY DIFFRACTIONr_angle_refined_deg2.4051.9851261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4495112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.47424.90251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59315194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.153158
X-RAY DIFFRACTIONr_chiral_restr0.1470.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02696
X-RAY DIFFRACTIONr_mcbond_it1.3631.5566
X-RAY DIFFRACTIONr_mcangle_it2.4342909
X-RAY DIFFRACTIONr_scbond_it4.0553377
X-RAY DIFFRACTIONr_scangle_it6.7224.5352
LS refinement shellResolution: 1.401→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 84 -
Rwork0.285 1388 -
all-1472 -
obs--89.43 %

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