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- PDB-4ooi: Reduced HlyU from Vibrio cholerae N16961 -

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Basic information

Entry
Database: PDB / ID: 4ooi
TitleReduced HlyU from Vibrio cholerae N16961
ComponentsTranscriptional activator HlyU
KeywordsDNA BINDING PROTEIN / Winged helix / DNA-binding domain / Hemolysin gene transcription regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator HlyU
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMukherjee, D. / Datta, A.B. / Chakrabarti, P.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Crystal structure of HlyU, the hemolysin gene transcription activator, from Vibrio cholerae N16961 and functional implications
Authors: Mukherjee, D. / Datta, A.B. / Chakrabarti, P.
History
DepositionFeb 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional activator HlyU
B: Transcriptional activator HlyU
C: Transcriptional activator HlyU
D: Transcriptional activator HlyU


Theoretical massNumber of molelcules
Total (without water)50,8874
Polymers50,8874
Non-polymers00
Water1,02757
1
A: Transcriptional activator HlyU
B: Transcriptional activator HlyU


Theoretical massNumber of molelcules
Total (without water)25,4442
Polymers25,4442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-32 kcal/mol
Surface area10020 Å2
MethodPISA
2
C: Transcriptional activator HlyU
D: Transcriptional activator HlyU


Theoretical massNumber of molelcules
Total (without water)25,4442
Polymers25,4442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-31 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.372, 41.721, 86.981
Angle α, β, γ (deg.)90.00, 92.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Transcriptional activator HlyU


Mass: 12721.831 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: serotype O1 str. N16961 / Gene: hlyU, VC_0678 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52695
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.86 Å3/Da / Density % sol: 33.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 8000, 0.05M potassium phosphate monobasic, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 5, 2012
RadiationMonochromator: Osmic Confocal Max-Flux optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→34.19 Å / Num. all: 18975 / Num. obs: 18570 / % possible obs: 97.49 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.78 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.316 Å / Redundancy: 3.81 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1744 / % possible all: 93

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JTH

3jth


Resolution: 2.2→34.19 Å / SU ML: 0.47 / σ(F): 1.35 / Phase error: 42.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3078 961 5.18 %RANDOM
Rwork0.258 ---
all0.2607 18975 --
obs0.2607 18570 96.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→34.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 0 57 3062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023029
X-RAY DIFFRACTIONf_angle_d0.6124068
X-RAY DIFFRACTIONf_dihedral_angle_d13.6881168
X-RAY DIFFRACTIONf_chiral_restr0.044492
X-RAY DIFFRACTIONf_plane_restr0.001507
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.3160.41351400.4002240893
2.316-2.46110.46811290.3992248396
2.4611-2.6510.35591210.3884248896
2.651-2.91770.43981450.3549251697
2.9177-3.33950.33371350.3012254297
3.3395-4.20630.29721340.2238257398
4.2063-34.19660.24851570.2001259997
Refinement TLS params.Method: refined / Origin x: 5.5314 Å / Origin y: 17.5686 Å / Origin z: 19.1269 Å
111213212223313233
T0.2395 Å2-0.0353 Å2-0.0884 Å2-0.2583 Å20.1203 Å2--0.23 Å2
L1.3295 °2-0.2726 °2-0.8401 °2-0.6388 °20.6629 °2--1.7007 °2
S0.0055 Å °-0.0958 Å °0.1666 Å °0.0338 Å °0.0654 Å °0.1538 Å °0.1044 Å °-0.2568 Å °-0.0513 Å °
Refinement TLS groupSelection details: all

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