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- PDB-3k79: C38A, C52V Cysteine-Free Variant of Rop (Rom) -

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Basic information

Entry
Database: PDB / ID: 3k79
TitleC38A, C52V Cysteine-Free Variant of Rop (Rom)
ComponentsRegulatory protein rop
KeywordsTRANSCRIPTION / hairpin / four-helix bundle / cysteine-free / Plasmid / Transcription regulation
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 / molecular replacement / Resolution: 1.96 Å
AuthorsHari, S.B. / Magliery, T.J.
CitationJournal: Protein Sci. / Year: 2010
Title: Cysteine-free Rop: a four-helix bundle core mutant has wild-type stability and structure but dramatically different unfolding kinetics.
Authors: Hari, S.B. / Byeon, C. / Lavinder, J.J. / Magliery, T.J.
History
DepositionOct 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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 1.3Sep 6, 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)7,1271
Polymers7,1271
Non-polymers00
Water1,24369
1
A: Regulatory protein rop

A: Regulatory protein rop


Theoretical massNumber of molelcules
Total (without water)14,2542
Polymers14,2542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area2720 Å2
ΔGint-28 kcal/mol
Surface area6270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.664, 40.304, 31.666
Angle α, β, γ (deg.)90.000, 101.970, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-75-

HOH

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Components

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


Mass: 7126.818 Da / Num. of mol.: 1 / Mutation: C38A, C52V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rop / Plasmid: pMR101 / 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.: 69 / 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: 1.96 Å3/Da / Density % sol: 37.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25-30% methanol, 100 mM MES, 300 mM NaCl, 10% glycerol, pH 5.7-5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 5.7-5.9

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.96→29.63 Å / Num. obs: 2675 / % possible obs: 66.1 % / Redundancy: 7.26 % / Rmerge(I) obs: 0.032 / Χ2: 0.97 / Net I/σ(I): 47.4 / Scaling rejects: 147
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.96-2.034.650.1679.3145310.927.7
2.03-2.115.740.15911.5419730.9917.8
2.11-2.26.60.12413.57791180.8430.9
2.2-2.327.030.1116.612801820.8643.2
2.32-2.467.040.07922.620652920.8374.5
2.46-2.657.520.0630.529293880.8895.6
2.65-2.927.60.03741.629213830.7496
2.92-3.347.580.02855.630944060.997.1
3.34-4.217.390.02667.328673831.1297.2
4.21-29.637.150.02188.130594191.3898.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.53 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.63 Å
Translation2.5 Å29.63 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.9Ldata scaling
PHASER2.1.1phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ROP

1rop


Resolution: 1.96→29.63 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.768 / SU ML: 0.31 / σ(F): 2.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 242 4.72 %
Rwork0.163 --
obs0.167 2675 65.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.655 Å2 / ksol: 0.459 e/Å3
Displacement parametersBiso max: 71.5 Å2 / Biso mean: 26.236 Å2 / Biso min: 11.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.242 Å2-0 Å2-3.651 Å2
2--2.252 Å2-0 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms454 0 0 69 523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013907
X-RAY DIFFRACTIONf_angle_d1.0881635
X-RAY DIFFRACTIONf_chiral_restr0.08571
X-RAY DIFFRACTIONf_plane_restr0.005142
X-RAY DIFFRACTIONf_dihedral_angle_d13.098232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-2.4640.34660.181272133834
2.464-29.630.2341760.1583613378997

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