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- PDB-3t1b: Crystal structure of the full-length AphB N100E variant -

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Basic information

Entry
Database: PDB / ID: 3t1b
TitleCrystal structure of the full-length AphB N100E variant
ComponentsTranscriptional regulator, LysR familyTranscriptional regulation
KeywordsTRANSCRIPTION / winged helix / virulence
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: 2.7 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 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)133,5174
Polymers133,5174
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14310 Å2
ΔGint-70 kcal/mol
Surface area51810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.737, 54.545, 103.840
Angle α, β, γ (deg.)90.00, 100.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 33379.238 Da / Num. of mol.: 4 / Mutation: N100E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 SEROGROUP O1 / Gene: aphB, VC_1049 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star / References: UniProt: Q9KT56
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 M sodium citrate, 0.1 M sodium cacodylate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 21, 2011
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→131.922 Å / Num. all: 58475 / Num. obs: 58215 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Redundancy: 7.5 % / Net I/σ(I): 15.64
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.24 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXAutoMRmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SZP

3szp


Resolution: 2.7→48.081 Å / SU ML: 0.71 / σ(F): 1.94 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 1406 3.42 %
Rwork0.197 --
obs0.1986 41165 99.8 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.942 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3817 Å2-0 Å27.9208 Å2
2---0.9333 Å20 Å2
3----1.4484 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9290 0 0 200 9490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029482
X-RAY DIFFRACTIONf_angle_d0.65112814
X-RAY DIFFRACTIONf_dihedral_angle_d14.6013642
X-RAY DIFFRACTIONf_chiral_restr0.0451440
X-RAY DIFFRACTIONf_plane_restr0.0021656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.79650.30041390.26293945X-RAY DIFFRACTION99
2.7965-2.90850.30871390.25613912X-RAY DIFFRACTION100
2.9085-3.04080.29241390.2473945X-RAY DIFFRACTION100
3.0408-3.20110.32021410.23183961X-RAY DIFFRACTION100
3.2011-3.40160.26071380.21143939X-RAY DIFFRACTION100
3.4016-3.66420.27291400.19883956X-RAY DIFFRACTION100
3.6642-4.03270.24411420.18293980X-RAY DIFFRACTION100
4.0327-4.61590.22181410.1623964X-RAY DIFFRACTION100
4.6159-5.81390.19571420.17484029X-RAY DIFFRACTION100
5.8139-48.08840.21081450.18364128X-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)
15.02510.5581-1.06452.56570.67462.7376-0.22980.62590.2013-0.0420.3187-0.0142-0.74370.0092-0.10590.5303-0.1056-0.04440.54960.08950.307228.51439.5138-76.6015
21.0406-0.0957-0.57381.91361.60393.4876-0.13390.7373-0.0839-0.16490.2135-0.0748-0.0662-0.1987-0.12320.3591-0.0334-0.04180.6434-0.01470.313433.19212.2326-73.936
33.6360.3252-1.14043.5644-0.50262.69530.0069-0.0090.02850.27410.1924-0.3181-0.08110.1702-0.11830.29220.0021-0.01170.1719-0.01340.180216.96024.6118-31.298
40.5685-0.85220.5561.72820.32073.19770.32320.17170.2889-0.3951-0.0446-0.1375-0.78650.3612-0.29040.396-0.05390.11860.3754-0.01180.375613.518718.2978-25.0195
54.1153-0.59710.4543.2608-0.77832.6396-0.03080.12650.1157-0.05720.0143-0.0414-0.0635-0.0171-0.00760.36180.00610.05360.2675-0.01470.226812.172317.0841-4.7194
60.9865-0.6521-0.75641.13571.52054.35030.160.34440.1613-0.4517-0.11380.0814-0.8421-0.4081-0.08580.4083-0.0350.03790.38920.06390.311310.037513.0191-29.2736
72.10891.845-0.86044.113-1.61080.95690.02530.101-0.2403-0.0398-0.0559-0.20990.05440.107-0.00010.28550.04110.04050.3484-0.07310.284834.419713.9647-8.7179
80.2517-0.08760.0432.09480.79672.4778-0.0699-0.0718-0.12870.11210.1762-0.11180.17360.2336-0.06150.32720.0330.02870.30130.02390.369520.4847-11.9789-16.4093
96.64760.2987-0.63613.3529-0.31974.86510.5476-0.53170.7350.27350.1044-0.4266-0.23590.2659-0.50260.3508-0.06620.03160.3569-0.01120.487935.280610.8474-55.0575
105.5688-0.48640.9495.37110.55083.6608-0.1045-0.25970.150.019-0.02660.21230.2663-0.05410.160.29590.07910.14990.2022-0.02020.468256.893519.793-62.0982
111.40761.97041.59616.2095.3124.52290.2642-0.0651-0.20250.2319-0.1052-0.75750.2634-0.1018-0.24250.3311-0.02150.15050.25530.0630.462770.130623.9513-48.6075
124.872-0.81990.63383.1421-0.00291.36010.05910.0157-0.36750.1457-0.0227-0.07920.06430.01620.01740.3391-0.03420.10930.23790.0060.404471.402132.314-39.9283
133.7908-2.59850.7212.8754-3.3147.4620.25790.3186-0.0652-0.7701-0.4716-0.29450.80290.07830.09260.46980.08080.1350.22620.0130.603364.16213.8393-65.662
140.4618-0.1163-0.59572.4029-2.02125.21310.0235-0.0183-0.01160.42890.1082-0.2055-0.2975-0.2855-0.10390.29480.0056-0.01010.3991-0.04710.481846.268631.9669-11.2978
150.5707-0.01530.75581.04890.15213.82390.1312-0.08350.1176-0.2338-0.08550.1747-0.4201-0.3374-0.06320.43930.06750.12280.2971-0.00090.552944.258837.9281-56.8008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:43)
2X-RAY DIFFRACTION2chain 'A' and (resseq 44:86)
3X-RAY DIFFRACTION3chain 'A' and (resseq 87:144)
4X-RAY DIFFRACTION4chain 'A' and (resseq 145:167)
5X-RAY DIFFRACTION5chain 'A' and (resseq 168:246)
6X-RAY DIFFRACTION6chain 'A' and (resseq 247:291)
7X-RAY DIFFRACTION7chain 'B' and (resseq 1:152)
8X-RAY DIFFRACTION8chain 'B' and (resseq 153:290)
9X-RAY DIFFRACTION9chain 'C' and (resseq 1:86)
10X-RAY DIFFRACTION10chain 'C' and (resseq 87:144)
11X-RAY DIFFRACTION11chain 'C' and (resseq 145:173)
12X-RAY DIFFRACTION12chain 'C' and (resseq 174:261)
13X-RAY DIFFRACTION13chain 'C' and (resseq 262:291)
14X-RAY DIFFRACTION14chain 'D' and (resseq 1:144)
15X-RAY DIFFRACTION15chain 'D' and (resseq 145:290)

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