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- PDB-7ets: Crystal structure of crp protein from Gardnerella Vaginalis -

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Basic information

Entry
Database: PDB / ID: 7ets
TitleCrystal structure of crp protein from Gardnerella Vaginalis
ComponentsCrp/Fnr family transcriptional regulator
KeywordsTRANSCRIPTION / cAMP receptor protein / Gardnerella Vaginalis
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold ...helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Crp/Fnr family transcriptional regulator
Similarity search - Component
Biological speciesGardnerella vaginalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsDong, H.J. / Wang, S. / Zhang, J.M. / Gu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of crp protein from Gardnerella Vaginalis
Authors: Dong, H.J. / Wang, S. / Zhang, J.M. / Gu, L.
History
DepositionMay 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Crp/Fnr family transcriptional regulator
B: Crp/Fnr family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8855
Polymers51,6642
Non-polymers2213
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-37 kcal/mol
Surface area21770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.953, 85.471, 56.022
Angle α, β, γ (deg.)90.000, 116.685, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Crp/Fnr family transcriptional regulator / cAMP receptor protein


Mass: 25831.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gardnerella vaginalis (bacteria)
Gene: AXE75_06165, CG405_03440, CYJ58_00485, CYJ65_00490, CYJ68_02605, EGX90_02820
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J8F7K9
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5% 2-propanol, 100mM Imidazole/Hydrochric acid, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.22→28 Å / Num. obs: 24348 / % possible obs: 98.29 % / Redundancy: 3.2 % / Biso Wilson estimate: 57.77 Å2 / CC1/2: 0.996 / Net I/σ(I): 2.318
Reflection shellResolution: 2.223→2.302 Å / Num. unique obs: 2226 / CC1/2: 0.947

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BYY

4byy


Resolution: 2.22→28 Å / SU ML: 0.3144 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.8201
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2759 1230 5.06 %
Rwork0.2382 23086 -
obs0.2402 24316 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.17 Å2
Refinement stepCycle: LAST / Resolution: 2.22→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3571 0 14 99 3684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263658
X-RAY DIFFRACTIONf_angle_d0.55484940
X-RAY DIFFRACTIONf_chiral_restr0.0407561
X-RAY DIFFRACTIONf_plane_restr0.0032638
X-RAY DIFFRACTIONf_dihedral_angle_d26.82831391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.310.391020.39362402X-RAY DIFFRACTION91.62
2.31-2.420.33671240.32592579X-RAY DIFFRACTION99.85
2.42-2.540.32661490.31812615X-RAY DIFFRACTION100
2.54-2.70.3451260.32172590X-RAY DIFFRACTION99.96
2.7-2.910.35131630.29672581X-RAY DIFFRACTION99.96
2.91-3.20.34121440.28982598X-RAY DIFFRACTION100
3.2-3.670.27571670.23862578X-RAY DIFFRACTION99.85
3.67-4.620.25021250.20892569X-RAY DIFFRACTION97.29
4.62-280.23661300.20232574X-RAY DIFFRACTION96.71

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