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- PDB-4knc: Structural and functional characterization of Pseudomonas aerugin... -

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Basic information

Entry
Database: PDB / ID: 4knc
TitleStructural and functional characterization of Pseudomonas aeruginosa AlgX
ComponentsAlginate biosynthesis protein AlgX
KeywordsSUGAR BINDING PROTEIN / alginate acetylation / SGNH hydrolase / carbohydrate-binding domain
Function / homology
Function and homology information


alginic acid biosynthetic process / single-species biofilm formation / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / periplasmic space
Similarity search - Function
C-terminal carbohydrate-binding module / Alginate biosynthesis protein AlgX, C-terminal carbohydrate-binding module / Alginate biosynthesis protein AlgX, N-terminal / AlgX, C-terminal domain superfamily / C-terminal carbohydrate-binding module / AlgX/AlgJ, SGNH hydrolase-like domain / SGNH hydrolase-like domain, acetyltransferase AlgX / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alginate biosynthesis protein AlgX
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.141 Å
AuthorsRiley, L.M. / Weadge, J.T. / Baker, P. / Robinson, H. / Codee, J.D.C. / Tipton, P.A. / Ohman, D.E. / Howell, P.L.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and Functional Characterization of Pseudomonas aeruginosa AlgX: ROLE OF AlgX IN ALGINATE ACETYLATION.
Authors: Riley, L.M. / Weadge, J.T. / Baker, P. / Robinson, H. / Codee, J.D. / Tipton, P.A. / Ohman, D.E. / Howell, P.L.
History
DepositionMay 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Alginate biosynthesis protein AlgX
A: Alginate biosynthesis protein AlgX


Theoretical massNumber of molelcules
Total (without water)102,0242
Polymers102,0242
Non-polymers00
Water6,702372
1
B: Alginate biosynthesis protein AlgX


Theoretical massNumber of molelcules
Total (without water)51,0121
Polymers51,0121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Alginate biosynthesis protein AlgX


Theoretical massNumber of molelcules
Total (without water)51,0121
Polymers51,0121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.697, 82.435, 92.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alginate biosynthesis protein AlgX


Mass: 51011.910 Da / Num. of mol.: 2 / Fragment: UNP residues 27-474
Source method: isolated from a genetically manipulated source
Details: codon-optimized synthetic algX gene prepared by GenScript Corporation, for expression in E. coli. Based on wild-type algX from P. aeruginosa PAO1
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: algX, PA3546 / Plasmid: pET-24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP / References: UniProt: Q51372
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 25% PEG3000, 100 mM sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2010
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.141→50 Å / Num. obs: 52346 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Rmerge(I) obs: 0.081 / Χ2: 1.802 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.141-2.239.80.6451641.0091100
2.23-2.329.70.52851571.2751100
2.32-2.429.80.36851921.0971100
2.42-2.559.90.27151671.1471100
2.55-2.719.80.20152091.3231100
2.71-2.929.80.13552051.5681100
2.92-3.219.80.09852181.8731100
3.21-3.689.60.07552572.5591100
3.68-4.639.30.06353133.246199.8
4.63-509.30.05554642.991198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.3phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.141→43.643 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7982 / SU ML: 0.24 / σ(F): 0 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1906 3.84 %RANDOM
Rwork0.176 ---
all0.1781 ---
obs0.1781 49660 93.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.09 Å2 / Biso mean: 50.108 Å2 / Biso min: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 2.141→43.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6504 0 0 372 6876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076767
X-RAY DIFFRACTIONf_angle_d1.0389143
X-RAY DIFFRACTIONf_chiral_restr0.07955
X-RAY DIFFRACTIONf_plane_restr0.0051200
X-RAY DIFFRACTIONf_dihedral_angle_d13.2392482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.141-2.19420.30551100.22012689279975
2.1942-2.25350.31281210.23073058317985
2.2535-2.31980.33011210.2353063318486
2.3198-2.39470.31121370.20143328346593
2.3947-2.48030.24981330.19553346347993
2.4803-2.57960.28811360.19773423355995
2.5796-2.69690.27561380.19713441357996
2.6969-2.83910.28891360.19453490362697
2.8391-3.01690.28261420.20333571371398
3.0169-3.24980.22661430.18463563370699
3.2498-3.57670.21791460.17133640378699
3.5767-4.09390.20161440.15553632377699
4.0939-5.15660.19481480.138737153863100
5.1566-43.65250.20691510.1813795394698
Refinement TLS params.Method: refined / Origin x: 143.8896 Å / Origin y: 15.1334 Å / Origin z: 38.1586 Å
111213212223313233
T0.2275 Å2-0.0244 Å20.0219 Å2-0.2777 Å20.0081 Å2--0.3312 Å2
L0.1246 °20.0378 °2-0.445 °2-0.3522 °20.0033 °2--1.8024 °2
S0.0026 Å °0.0417 Å °0.1124 Å °-0.0072 Å °0.0221 Å °0.0764 Å °0.019 Å °-0.1319 Å °-0.0233 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB42 - 686
2X-RAY DIFFRACTION1allA41 - 688

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