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- PDB-2iji: Structure of F14H mutant of ColE1 Rom protein -

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Basic information

Entry
Database: PDB / ID: 2iji
TitleStructure of F14H mutant of ColE1 Rom protein
ComponentsRegulatory protein rop
KeywordsTRANSCRIPTION REGULATOR / Rom / Rop / ColE1 plasmid copy control
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStruble, E.B.
CitationJournal: Proteins / Year: 2008
Title: New crystal structures of ColE1 Rom and variants resulting from mutation of a surface exposed residue: Implications for RNA-recognition.
Authors: Struble, E.B. / Ladner, J.E. / Brabazon, D.M. / Marino, J.P.
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein rop


Theoretical massNumber of molelcules
Total (without water)7,1541
Polymers7,1541
Non-polymers00
Water23413
1
A: Regulatory protein rop

A: Regulatory protein rop


Theoretical massNumber of molelcules
Total (without water)14,3082
Polymers14,3082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2640 Å2
ΔGint-26 kcal/mol
Surface area6110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)39.140, 39.140, 57.442
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 7153.868 Da / Num. of mol.: 1 / Mutation: M1G, F14H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rop / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P03051
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.78 Å3/Da / Density % sol: 30.72 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: 1uL protein solution (0.5-1 mM) was mixed with 1 uL well buffer (0.1M sodium acetate pH 5.5, 0.1M sodium chloride, 37 40% ethanol, and 20% glycerol), VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 12, 2005 / Details: Blue Max-flux confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→33.1 Å / Num. obs: 2378 / % possible obs: 96.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.44 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 2.3 / Num. unique all: 222 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASER1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ROP

1rop


Resolution: 2.3→33.1 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.911 / SU B: 14.505 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.664 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29163 93 4.1 %RANDOM
Rwork0.23435 ---
obs0.23675 2157 91.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.312 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0.59 Å20 Å2
2---1.18 Å20 Å2
3---1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms444 0 0 13 457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021448
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3451.96603
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.129555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49524.825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0411583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.84154
X-RAY DIFFRACTIONr_chiral_restr0.1310.270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02337
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.2199
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.2289
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3210.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3820.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0911.5291
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.992441
X-RAY DIFFRACTIONr_scbond_it3.0723177
X-RAY DIFFRACTIONr_scangle_it5.0764.5162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 6 -
Rwork0.427 146 -
obs--97.44 %

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