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- PDB-7kae: Rop protein variant with a buried tryptophan -

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Basic information

Entry
Database: PDB / ID: 7kae
TitleRop protein variant with a buried tryptophan
ComponentsRegulatory protein rop
KeywordsRNA BINDING PROTEIN / helical bundle / engineering / substitution / absorbance
Function / homologyRegulatory protein Rop / Rop-like superfamily / Rop protein / identical protein binding / Regulatory protein rop
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGallagher, D.T. / Hoopes, J.T. / Karageorgos, I.
CitationJournal: To be published
Title: Structure of a Rop protein variant with a buried tryptophan
Authors: Hoopes, J.T. / Karageorgos, I. / Gallagher, D.T.
History
DepositionSep 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,0492
Polymers15,0492
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-23 kcal/mol
Surface area6020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.881, 40.016, 72.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 7524.258 Da / Num. of mol.: 2 / Fragment: engineered variant / Mutation: R16Q, S17N, L20Q, C38A, C52A, F56W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rop / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03051
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 30.58 % / Description: rectangular bar
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 28% (w/v) PEG 400, 300 mM NaCl, 100 mM NaHEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→36.14 Å / Num. obs: 14720 / % possible obs: 96.8 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.016 / Rrim(I) all: 0.044 / Net I/σ(I): 14.7
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 690 / CC1/2: 0.97 / Rrim(I) all: 0.243

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rop

1rop


Resolution: 1.6→12 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.165 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 688 4.8 %RANDOM
Rwork0.1942 ---
obs0.1956 13516 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.19 Å2 / Biso mean: 27.255 Å2 / Biso min: 15.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0 Å2
2---1.31 Å20 Å2
3---1.4 Å2
Refinement stepCycle: final / Resolution: 1.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms899 0 0 66 965
Biso mean---36.52 -
Num. residues----113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.012937
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.6431264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2445111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14823.96863
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98515178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.141157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02732
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 48 -
Rwork0.179 940 -
all-988 -
obs--95.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.07241.72681.43942.4481.08472.10570.0544-0.17660.18450.2002-0.1320.2510.0014-0.26290.07760.0470.03070.020.0767-0.01020.02717.07197.199819.912
21.90811.02460.72762.10.40861.4277-0.04270.09310.0572-0.02640.0555-0.0415-0.0250.0048-0.01280.03060.0126-0.01820.0336-0.00660.016316.07537.626415.5658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 57
2X-RAY DIFFRACTION2B2 - 57

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