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- PDB-9gfp: The crystal structure of CsvR from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 9gfp
TitleThe crystal structure of CsvR from Escherichia coli
ComponentsHTH-type transcriptional activator CsvR
KeywordsTRANSCRIPTION / transcription activation HTH-type
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeobox-like domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional activator CsvR
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsMoche, M. / Joffre, E. / Ampah-Korsah, H. / Nyman, T. / Sjoling, A. / Sun, L.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2020-01941 Sweden
Swedish Research Council2023-03028 Sweden
CitationJournal: To Be Published
Title: The crystal structure of CsvR from Escherichia coli
Authors: Moche, M. / Sjoling, A. / Ampah-Korsah, H. / Nyman, T. / Joffre, E. / Sun, L.
History
DepositionAug 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional activator CsvR
B: HTH-type transcriptional activator CsvR


Theoretical massNumber of molelcules
Total (without water)62,2952
Polymers62,2952
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-10 kcal/mol
Surface area24920 Å2
Unit cell
Length a, b, c (Å)42.613, 77.601, 184.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HTH-type transcriptional activator CsvR


Mass: 31147.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: csvR / Variant: T1R pRARE2 / Plasmid: pNIC-MBP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P43460
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 %w/v PEG3350 0.15 M DL-malic 7 pH 6 %w/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 3.03→48.32 Å / Num. obs: 8763 / % possible obs: 69.8 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.051 / Rrim(I) all: 0.183 / Net I/σ(I): 10.1
Reflection shellResolution: 3.03→3.285 Å / Redundancy: 13 % / Rmerge(I) obs: 2.748 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 438 / CC1/2: 0.454 / Rpim(I) all: 0.791 / Rrim(I) all: 2.861 / % possible all: 16.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.03→48.32 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / SU B: 72.906 / SU ML: 0.573 / Cross valid method: THROUGHOUT / ESU R Free: 0.72 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29781 403 4.6 %RANDOM
Rwork0.21225 ---
obs0.21641 8360 69.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 147.964 Å2
Baniso -1Baniso -2Baniso -3
1--7.42 Å2-0 Å2-0 Å2
2--1.84 Å2-0 Å2
3---5.58 Å2
Refinement stepCycle: 1 / Resolution: 3.03→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4047 0 0 9 4056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124109
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164105
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.825516
X-RAY DIFFRACTIONr_angle_other_deg0.5161.7719411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1415492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.66527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.82110824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02979
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_it6.3436.9681980
X-RAY DIFFRACTIONr_mcbond_other6.3416.9681980
X-RAY DIFFRACTIONr_mcangle_it10.51312.5052468
X-RAY DIFFRACTIONr_mcangle_other10.51112.5072469
X-RAY DIFFRACTIONr_scbond_it6.9847.4592129
X-RAY DIFFRACTIONr_scbond_other6.9837.462130
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.7713.5213049
X-RAY DIFFRACTIONr_long_range_B_refined19.69884.5917409
X-RAY DIFFRACTIONr_long_range_B_other19.69784.5917410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.03→3.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.547 1 -
Rwork0.305 52 -
obs--5.95 %
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)
16.207-3.54973.15226.0126-1.98482.8766-0.1480.0565-0.03470.38420.11190.0391-0.26610.01520.03610.3238-0.05780.05240.0228-0.01430.014821.24417.719344.6825
24.40821.64122.36021.9130.33522.8022-0.13061.4222-0.3364-0.98020.2913-0.36450.69160.0023-0.16072.02880.0664-0.41281.1705-0.28530.7389-0.54172.38086.4976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 265
2X-RAY DIFFRACTION2B10 - 265

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