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- PDB-4k2e: HlyU from Vibrio cholerae N16961 -

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Basic information

Entry
Database: PDB / ID: 4k2e
TitleHlyU from Vibrio cholerae N16961
ComponentsTranscriptional activator HlyU
KeywordsTRANSCRIPTION ACTIVATOR / Winged helix / DNA-binding domain / Hemolysin gene transcription regulator / DNA / S-HYDROXYCYSTEINE
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 ...: / 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: 1.8 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
DepositionApr 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)50,9514
Polymers50,9514
Non-polymers00
Water3,657203
1
A: Transcriptional activator HlyU
B: Transcriptional activator HlyU


Theoretical massNumber of molelcules
Total (without water)25,4762
Polymers25,4762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-32 kcal/mol
Surface area9820 Å2
MethodPISA
2
C: Transcriptional activator HlyU
D: Transcriptional activator HlyU


Theoretical massNumber of molelcules
Total (without water)25,4762
Polymers25,4762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-27 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.334, 42.188, 88.288
Angle α, β, γ (deg.)90.00, 93.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Transcriptional activator HlyU


Mass: 12737.831 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: 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.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 36.58 %
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: Jul 16, 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: 1.8→26.531 Å / Num. all: 36629 / Num. obs: 36262 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.75 % / Biso Wilson estimate: 37.15 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.69 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 1.8 / % possible all: 99.86

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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: 1.8→26.53 Å / SU ML: 0.26 / σ(F): 2 / Phase error: 28.22 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 1816 5.01 %RANDOM
Rwork0.1894 ---
all0.1919 36629 --
obs0.1919 36213 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→26.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 0 203 3187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113024
X-RAY DIFFRACTIONf_angle_d1.3034062
X-RAY DIFFRACTIONf_dihedral_angle_d19.0521174
X-RAY DIFFRACTIONf_chiral_restr0.092490
X-RAY DIFFRACTIONf_plane_restr0.005506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.84870.3241340.32472664100
1.8487-1.90310.34921390.30232648100
1.9031-1.96450.29471180.28232671100
1.9645-2.03470.30221340.24482643100
2.0347-2.11610.26021410.2152680100
2.1161-2.21230.29441350.20292634100
2.2123-2.32890.27151520.1944261699
2.3289-2.47470.25391410.2038266599
2.4747-2.66560.28971410.2128263999
2.6656-2.93360.2521410.2069264999
2.9336-3.35740.22081490.1901265899
3.3574-4.22720.20331350.1529265097
4.2272-26.5340.22181560.1707258094
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)
17.78740.01781.52386.45941.16986.0715-0.1118-0.3535-0.21670.56730.25070.2819-0.1057-0.3917-0.17330.3104-0.00120.00750.2827-0.03360.242917.229211.19350.4196
22.12952.37841.16563.8406-0.61388.7430.04050.52750.3211-1.150.2352-0.115-0.4824-0.1229-0.19680.49660.04580.05710.33920.02180.316221.071515.1729-13.8146
38.6855-0.61022.64093.50852.36536.54390.07150.7687-0.0407-1.0458-0.12990.21950.4988-0.3311-0.0980.6429-0.067-0.0830.35350.03170.34612.32328.1554-14.9189
47.69213.40851.47425.24245.06815.7503-0.5510.14190.7927-0.1408-0.08671.5584-0.6226-0.74610.64380.42690.0318-0.0470.57030.02510.44939.155617.87541.5841
58.0105-0.1985-0.94465.69572.69051.7862-0.11631.3691.4702-1.14360.0810.8572-0.7442-0.1946-0.10870.5338-0.0301-0.10390.54820.12940.491220.296322.82732.2993
64.68970.1581.21495.6031-0.73078.53510.3531-0.2304-0.48850.3863-0.01710.22660.4716-0.4109-0.35580.3435-0.0126-0.02050.31370.03140.269822.038910.656720.9225
75.0004-4.53426.25554.5941-5.79858.2596-0.271-0.08230.15480.68070.0187-0.6449-0.45450.42550.14350.3617-0.00380.01120.36160.01530.316429.956317.115817.3614
85.29260.2433-2.84828.8131-0.15852.6378-0.2703-1.09610.44020.87120.27320.0089-0.5628-0.4264-0.01240.38240.09030.06140.4283-0.05250.264522.545522.039625.7562
99.76561.37123.7313.39725.42868.94970.144-0.8513-0.30060.2691-0.35730.77660.8999-0.73940.28180.43930.02380.05660.60510.09680.349410.977112.88611.6703
106.98820.52530.37546.46950.16127.684-0.19710.26140.4583-0.9188-0.0089-0.0381-0.19960.07440.10110.330.024-0.03140.34220.00160.2494-12.158126.94835.8595
115.41171.4049-1.67745.3456-0.54914.9111-0.2346-0.1565-0.0788-0.00050.1370.94091.1897-1.33360.07850.4762-0.1751-0.01850.49660.03230.4-25.189617.007242.5864
124.1359-3.45163.43218.0792-2.00943.45640.2685-0.2662-0.5294-0.51740.15720.22980.585-0.0079-0.52120.5649-0.0496-0.09760.45220.02340.3477-11.483216.756730.4011
139.2479-2.7429-0.04991.96520.38953.6587-0.0782-0.5923-1.0591-0.1977-0.09380.78381.27470.23790.06840.51860.00340.0120.34790.01450.372-5.162418.184940.0866
148.70530.2928-4.00739.48011.21368.44810.15550.47081.17-0.16560.02430.32880.04810.0224-0.21960.3055-0.0759-0.04820.35930.08270.394-1.54834.297230.8769
158.5604-1.6769-2.65492.88910.28249.62090.6321.11781.7993-1.1096-0.3558-1.0945-1.4139-0.1634-0.04460.75280.0180.02460.59120.26430.74775.436938.077824.3331
164.6872-4.29221.70074.1156-2.11332.9483-0.1864-0.83430.88840.4893-0.1702-0.3174-1.5590.18010.4490.7405-0.1164-0.08290.574-0.02690.5557.053234.661936.9533
173.2982.433-3.34798.2342-2.60173.4647-0.0427-0.2658-0.2231-0.6037-0.3324-1.385-0.27640.99250.18420.5145-0.0190.09810.64140.12920.565912.600430.277927.3149
183.6285-2.3481-0.23858.43033.48432.99080.16670.7846-0.0931-0.9777-0.1370.45060.05390.1877-0.01040.584-0.0621-0.06590.48010.03920.3476-6.964725.546925.089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 11:46 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 47:70 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 71:89 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 90:105 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 14:28 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 29:57 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 58:71 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 72:89 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 90:105 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 11:40 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 41:89 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 90:105 )
13X-RAY DIFFRACTION13CHAIN D AND (RESID 14:28 )
14X-RAY DIFFRACTION14CHAIN D AND (RESID 29:40 )
15X-RAY DIFFRACTION15CHAIN D AND (RESID 41:57 )
16X-RAY DIFFRACTION16CHAIN D AND (RESID 58:71 )
17X-RAY DIFFRACTION17CHAIN D AND (RESID 72:89 )
18X-RAY DIFFRACTION18CHAIN D AND (RESID 90:105 )

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