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- PDB-3qoq: Crystal Structure of the Transcription Factor AmrZ in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 3qoq
TitleCrystal Structure of the Transcription Factor AmrZ in Complex with the 18 Base Pair amrZ1 Binding Site
Components
  • Alginate and motility regulator Z
  • DNA (5'-D(*AP*CP*TP*GP*GP*CP*AP*AP*AP*AP*CP*GP*CP*CP*GP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*CP*GP*GP*CP*GP*TP*TP*TP*TP*GP*CP*CP*AP*GP*T)-3')
KeywordsTranscription/DNA / Protein-DNA Complex / Ribbon-Helix-Helix / Transcription Factor / DNA Binding / Transcription-DNA complex
Function / homology
Function and homology information


cis-regulatory region sequence-specific DNA binding => GO:0000987 / regulation of polysaccharide biosynthetic process / negative regulation of single-species biofilm formation on inanimate substrate / negative regulation of bacterial-type flagellum-dependent cell motility / positive regulation of single-species biofilm formation on inanimate substrate / type IV pilus-dependent motility / positive regulation of cell motility / DNA-binding transcription repressor activity / bacterial-type flagellum assembly / : ...cis-regulatory region sequence-specific DNA binding => GO:0000987 / regulation of polysaccharide biosynthetic process / negative regulation of single-species biofilm formation on inanimate substrate / negative regulation of bacterial-type flagellum-dependent cell motility / positive regulation of single-species biofilm formation on inanimate substrate / type IV pilus-dependent motility / positive regulation of cell motility / DNA-binding transcription repressor activity / bacterial-type flagellum assembly / : / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Arc-like DNA binding domain / Arc-like DNA binding domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor AmrZ / Alginate and motility regulator Z
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsPryor Jr., E.E. / Wozniak, D.J. / Hollis, T.
CitationJournal: Plos Pathog. / Year: 2012
Title: The Transcription Factor AmrZ Utilizes Multiple DNA Binding Modes to Recognize Activator and Repressor Sequences of Pseudomonas aeruginosa Virulence Genes.
Authors: Pryor Jr., E.E. / Waligora, E.A. / Xu, B. / Dellos-Nolan, S. / Wozniak, D.J. / Hollis, T.
History
DepositionFeb 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alginate and motility regulator Z
B: Alginate and motility regulator Z
C: Alginate and motility regulator Z
D: Alginate and motility regulator Z
E: DNA (5'-D(*AP*CP*TP*GP*GP*CP*AP*AP*AP*AP*CP*GP*CP*CP*GP*GP*CP*A)-3')
F: DNA (5'-D(*TP*GP*CP*CP*GP*GP*CP*GP*TP*TP*TP*TP*GP*CP*CP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)42,6606
Polymers42,6606
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12030 Å2
ΔGint-77 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.465, 129.465, 152.554
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein
Alginate and motility regulator Z / DNA binding-protein


Mass: 7906.509 Da / Num. of mol.: 4 / Fragment: UNP residues 1-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: algZ, amrZ, PA3385 / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9RPY7, UniProt: G3XCY4*PLUS
#2: DNA chain DNA (5'-D(*AP*CP*TP*GP*GP*CP*AP*AP*AP*AP*CP*GP*CP*CP*GP*GP*CP*A)-3')


Mass: 5519.596 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*GP*CP*CP*GP*GP*CP*GP*TP*TP*TP*TP*GP*CP*CP*AP*GP*T)-3')


Mass: 5514.550 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.75 Å3/Da / Density % sol: 67.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3% PEG8K, 0.1M MES, 0.15M NaCl, 2mM TCEP, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2009
RadiationMonochromator: SILICON(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 11900 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.069 / Χ2: 1.308 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.155.80.54311410.8941100
3.15-3.215.80.28311391.0021100
3.21-3.275.70.19510961.0661100
3.27-3.345.70.20911281.075199.8
3.34-3.415.80.21311470.9761100
3.41-3.495.80.16211101.0951100
3.49-3.585.80.15611091.0221100
3.58-3.685.80.15711211.0311100
3.68-3.785.70.13511190.9811100
3.78-3.915.80.10311371.0481100
3.91-4.045.80.0811331.03199.9
4.04-4.215.80.07510891.0671100
4.21-4.45.80.06211341.186199.9
4.4-4.635.70.05611261.237199.9
4.63-4.925.70.05611201.581199.9
4.92-5.35.70.05911171.8199.9
5.3-5.835.70.05511282.109199.9
5.83-6.675.60.0511322.091199.7
6.67-8.395.50.03511191.913199.6
8.39-405.70.02810902.082196.2

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
112.859-16.172-52.504SE68.122.67
2-59.81117.136-38.985SE68.962.09
3-59.92333.221-41.407SE62.371.98
4-31.75116.122-95.93SE60.751.66
5-24.51324.691-53.622SE62.81.78
6-28.8334.965-43.354SE50.80.66
74.07-41.007-40.379SE62.051.33
8-18.03213.027-59.557SE56.510.99
9-2.67-29.09-42.996SE54.240.93
10-4.677-46.295-35.708SE56.130.97
11-10.971-18.946-60.314SE55.460.91
12-4.091-28.054-45.467SE54.610.93
13-5.413-29.7-33.94SE54.580.81
14-17.384-30.431-97.141SE52.780.74
Phasing dmFOM : 0.65 / FOM acentric: 0.67 / FOM centric: 0.57 / Reflection: 11828 / Reflection acentric: 10269 / Reflection centric: 1559
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.9-39.2480.940.960.89558379179
5.5-8.90.870.90.7416541336318
4.4-5.50.830.860.6520231724299
3.9-4.40.760.770.6220091777232
3.3-3.90.540.560.3734773131346
3.1-3.30.320.340.221071922185

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.14phasing
REFMACrefmac_5.5.0063refinement
PDB_EXTRACT3.1data extraction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.1→39.25 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.295 / WRfactor Rwork: 0.261 / Occupancy max: 1 / Occupancy min: 1 / SU B: 18.656 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2954 593 5 %RANDOM
Rwork0.2614 ---
obs0.2631 11827 100 %-
all-11827 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.96 Å2 / Biso mean: 82.8186 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2---1.1 Å20 Å2
3---2.2 Å2
Refinement stepCycle: LAST / Resolution: 3.1→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 732 0 7 2261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212356
X-RAY DIFFRACTIONr_angle_refined_deg1.182.3523316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2935187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95323.01283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.31415298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4031522
X-RAY DIFFRACTIONr_chiral_restr0.0630.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1-3.180.446530.317759812
3.18-3.2670.312400.299775815
3.267-3.3610.381260.303756782
3.361-3.4630.373490.31734783
3.463-3.5760.312450.311726771
3.576-3.7010.366350.274711746
3.701-3.8390.301340.273685719
3.839-3.9940.272480.245647695
3.994-4.170.324350.239625660
4.17-4.3710.218300.24620650
4.371-4.6040.283280.235589617
4.604-4.8790.345280.229557585
4.879-5.210.286260.237535561
5.21-5.6190.267250.276494519
5.619-6.1430.214260.286460486
6.143-6.8470.308160.297428444
6.847-7.8670.247180.256380398
7.867-9.540.286130.216328341
9.54-13.1090.359140.229268282
13.109-39.2480.10140.268157161

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