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- PDB-3szp: Full-length structure of the Vibrio cholerae virulence activator,... -

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Basic information

Entry
Database: PDB / ID: 3szp
TitleFull-length structure of the Vibrio cholerae virulence activator, AphB, a member of the LTTR protein family
ComponentsTranscriptional regulator, LysR familyTranscriptional regulation
KeywordsTRANSCRIPTION / winged helix-turn helix / DNA-binding / transcription factor
Function / homology
Function and homology information


DNA-binding transcription repressor activity / DNA-binding transcription activator activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA-templated transcription
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / D-Maltodextrin-Binding Protein; domain 2 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator, LysR family
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsTaylor, J.L. / De Silva, R.S. / Kovacikova, G. / Lin, W. / Taylor, R.K. / Skorupski, K. / Kull, F.J.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: The crystal structure of AphB, a virulence gene activator from Vibrio cholerae, reveals residues that influence its response to oxygen and pH.
Authors: Taylor, J.L. / De Silva, R.S. / Kovacikova, G. / Lin, W. / Taylor, R.K. / Skorupski, K. / Kull, F.J.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, LysR family
B: Transcriptional regulator, LysR family


Theoretical massNumber of molelcules
Total (without water)66,7282
Polymers66,7282
Non-polymers00
Water6,287349
1
A: Transcriptional regulator, LysR family
B: Transcriptional regulator, LysR family

A: Transcriptional regulator, LysR family
B: Transcriptional regulator, LysR family


Theoretical massNumber of molelcules
Total (without water)133,4574
Polymers133,4574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area14100 Å2
ΔGint-86 kcal/mol
Surface area50760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.209, 106.100, 167.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Transcriptional regulator, LysR family / Transcriptional regulation / AphB / LysR-type transcriptional regulator


Mass: 33364.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_1049 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9KT56
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 3.34 Å3/Da / Density % sol: 63.21 %
Description: R MEASURED = 0.089 (0.416 FOR HIGHEST RESOLUTION SHELL)
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 4 M sodium formate, 0.01 M betaine monohydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2006
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→48.9 Å / Num. all: 45623 / Num. obs: 45546 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Net I/σ(I): 13.12
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 7282 / % possible all: 99.4

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHENIXAutoMRmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEMET DERIVATIVE SOLVED BY SAD

Resolution: 2.202→48.85 Å / SU ML: 0.6 / σ(F): 2.01 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 2277 5 %RANDOM
Rwork0.208 ---
obs0.2093 45542 99.84 %-
all-45623 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.921 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1645 Å2-0 Å20 Å2
2---3.4311 Å2-0 Å2
3---6.5956 Å2
Refinement stepCycle: LAST / Resolution: 2.202→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4629 0 0 349 4978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084718
X-RAY DIFFRACTIONf_angle_d1.1126377
X-RAY DIFFRACTIONf_dihedral_angle_d14.4241807
X-RAY DIFFRACTIONf_chiral_restr0.073718
X-RAY DIFFRACTIONf_plane_restr0.004824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2019-2.28060.30552240.2644251X-RAY DIFFRACTION99
2.2806-2.3720.2872250.25164274X-RAY DIFFRACTION100
2.372-2.47990.27882250.25084272X-RAY DIFFRACTION100
2.4799-2.61060.28492260.24314305X-RAY DIFFRACTION100
2.6106-2.77420.25632260.23654292X-RAY DIFFRACTION100
2.7742-2.98840.24932260.23154284X-RAY DIFFRACTION100
2.9884-3.2890.24632280.21334337X-RAY DIFFRACTION100
3.289-3.76480.21112290.18674345X-RAY DIFFRACTION100
3.7648-4.74270.20822300.16864378X-RAY DIFFRACTION100
4.7427-48.86250.20982380.20254527X-RAY DIFFRACTION100
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)
15.71031.6326-1.09410.7515-0.17883.7696-0.0718-0.189-0.32550.0567-0.04640.00450.21290.05550.13120.20890.0415-0.02560.22040.01170.320645.9387-35.2184-26.4331
20.0986-0.11360.32720.1117-0.36241.1087-0.2114-1.29030.99940.42620.48120.2115-0.21480.0027-0.13610.45940.09850.05680.517-0.28020.913632.8116-20.1333-16.5948
33.70380.7177-0.44424.16540.4614.28950.0528-0.4220.03410.4594-0.0557-0.5259-0.04960.4976-0.0670.19380.0131-0.01670.2919-0.00030.19918.6859-37.6569-14.9706
42.85361.308-1.32623.2873-0.47463.26-0.03990.0228-0.13480.008-0.170.1691-0.2274-0.6680.13220.19840.0446-0.02390.3092-0.06260.170812.6025-64.3949-16.3055
53.0121-2.7785-1.42054.0087-0.81713.82530.114-0.39050.42760.90140.0274-0.0558-0.8626-0.1001-0.08360.42460.0416-0.03370.3593-0.09690.278613.844-32.5233-9.6887
60.8545-0.52080.54450.3887-0.60511.2224-0.17860.7338-0.8175-0.223-0.2835-0.44160.66330.4249-0.6627-0.0330.33190.18490.3784-0.37191.902867.1198-94.0991-32.7966
70.8324-0.0193-0.02840.34570.45031.07720.0257-0.4617-0.79630.4256-0.1858-1.05180.4862-0.0184-0.10520.3275-0.00090.02240.19230.24281.150849.4468-86.3677-23.9282
83.9137-0.1262-0.94044.51380.01863.44890.07550.13990.272-0.0054-0.0361-0.3429-0.26950.04950.00260.19310.0172-0.02570.1394-0.01280.167729.6746-58.237-31.5654
92.8162-0.6928-0.67143.3875-1.80155.3046-0.05210.1953-0.1176-0.4109-0.01990.0730.2663-0.09380.02790.21890.00210.0090.15620.02140.174718.5982-35.3916-38.9343
102.90192.7149-2.01174.9286-0.05362.98440.02180.389-0.0167-0.6792-0.0855-0.1862-0.1616-0.21980.03360.20920.02520.01790.1956-0.0270.155633.2518-65.5795-37.619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:68)
2X-RAY DIFFRACTION2(chain A and resid 69:90)
3X-RAY DIFFRACTION3(chain A and resid 91:160)
4X-RAY DIFFRACTION4(chain A and resid 161:260)
5X-RAY DIFFRACTION5(chain A and resid 261:290)
6X-RAY DIFFRACTION6(chain B and resid 1:59)
7X-RAY DIFFRACTION7(chain B and resid 60:94)
8X-RAY DIFFRACTION8(chain B and resid 95:159)
9X-RAY DIFFRACTION9(chain B and resid 160:262)
10X-RAY DIFFRACTION10(chain B and resid 263:290)

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