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- PDB-9cfs: Structure of a 150% lengthened variant of the E. coli ROP protein -

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Basic information

Entry
Database: PDB / ID: 9cfs
TitleStructure of a 150% lengthened variant of the E. coli ROP protein
ComponentsLong regulatory protein rop
KeywordsRNA BINDING PROTEIN / 4-helix bundle / engineered / extended / ROM
Function / homologyNICKEL (II) ION
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGallagher, D.T. / Shakya, A.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structure of an engineered 150% lengthened variant of the E.coli ROP protein
Authors: Gallagher, D.T. / Shakya, A.
History
DepositionJun 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Long regulatory protein rop
B: Long regulatory protein rop
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6593
Polymers21,6012
Non-polymers591
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-50 kcal/mol
Surface area8950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.253, 43.253, 84.158
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Long regulatory protein rop


Mass: 10800.343 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.54 % / Description: hexagonal prism
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 200 mM Na Phosphate 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.75→22.45 Å / Num. obs: 17737 / % possible obs: 99.7 % / Redundancy: 7.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.044 / Rrim(I) all: 0.129 / Χ2: 0.92 / Net I/σ(I): 10.9 / Num. measured all: 138359
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 96.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.407 / Num. measured all: 4404 / Num. unique obs: 942 / CC1/2: 0.817 / Rpim(I) all: 0.205 / Rrim(I) all: 0.458 / Χ2: 0.45 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PHASERphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→22.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.018 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25602 880 5 %RANDOM
Rwork0.1994 ---
obs0.20211 16826 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.644 Å2
Baniso -1Baniso -2Baniso -3
1--5.09 Å2-0 Å2-0 Å2
2---5.09 Å2-0 Å2
3---10.17 Å2
Refinement stepCycle: 1 / Resolution: 1.75→22.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 1 139 1502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121382
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.6431846
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9565168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00426.57170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7915292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.152152
X-RAY DIFFRACTIONr_chiral_restr0.1260.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021024
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4631.687678
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9572.519844
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6312.084704
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.69826.582275
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 45 -
Rwork0.166 1244 -
obs--96.77 %
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)
13.08881.8910.06331.6346-0.34850.3168-0.06370.1125-0.1039-0.05210.0648-0.06510.0170.0028-0.00110.0594-0.03640.00010.0742-0.00560.0045.79129.9996-4.3578
22.49851.402-0.3460.9289-0.05730.1970.2089-0.3783-0.18070.2413-0.2056-0.10670.07570.0987-0.00330.1294-0.0458-0.01010.1305-0.00150.07085.10669.07714.6898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 85
2X-RAY DIFFRACTION2B1 - 85

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